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72 hits found for Nucleic Acids Res

SASDBZ3 – Aureochrome 1a bZIP-LOV module: PtAUREO1a bZIP-LOV (Light oxygen voltage)/DNA complex (light state)

Aureobox dsDNAAureochrome 1a bZIP-LOV module experimental SAS data
DAMFILT model
Sample: Aureobox dsDNA monomer, synthetic construct DNA
Aureochrome 1a bZIP-LOV module dimer, Phaeodactylum tricornutum protein
Buffer: 50 mM Tris 50 mM boric acid 1 mM EDTA, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2014 Nov 6
...responsive domains of diatom class I aureochromes. Nucleic Acids Res 44(12):5957-70 (2016)
Banerjee A, Herman E, Serif M, Maestre-Reyna M, Hepp S, Pokorny R, Kroth PG, Essen LO, Kottke T
RgGuinier 4.5 nm
Dmax 16.7 nm
VolumePorod 97 nm3

SASDC62 – Basic domain of telomeric repeat-binding factor 2 (TRF2)

Basic domain of telomeric repeat-binding factor 2 experimental SAS data
Basic domain of telomeric repeat-binding factor 2 Kratky plot
Sample: Basic domain of telomeric repeat-binding factor 2 monomer, Homo sapiens protein
Buffer: 50 mM NaPi, 50 mM NaCl, pH: 7
Experiment: SAXS data collected at Rigaku BioSAXS-1000, CEITEC on 2015 Mar 5
...restores it. Nucleic Acids Res 45(21):12170-12180 (2017)
Necasová I, Janoušková E, Klumpler T, Hofr C
RgGuinier 1.7 nm
Dmax 7.1 nm
VolumePorod 4 nm3

SASDB24 – Aureochrome 1a bZIP-LOV module: PtAUREO1a bZIP-LOV (Light oxygen voltage) module (light state, Tris)

Aureochrome 1a bZIP-LOV module experimental SAS data
Aureochrome 1a bZIP-LOV module Kratky plot
Sample: Aureochrome 1a bZIP-LOV module dimer, Phaeodactylum tricornutum protein
Buffer: 10 mM Tris 300 mM NaCl, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2014 Nov 6
...responsive domains of diatom class I aureochromes. Nucleic Acids Res 44(12):5957-70 (2016)
Banerjee A, Herman E, Serif M, Maestre-Reyna M, Hepp S, Pokorny R, Kroth PG, Essen LO, Kottke T
RgGuinier 3.9 nm
Dmax 12.5 nm
VolumePorod 121 nm3

SASDAQ8 – kLANA mutant dimer-tetramer mixture

ORF73 tetramerORF73 dimer experimental SAS data
NONE model
Sample: ORF73 tetramer tetramer, Human herpesvirus 8 protein
ORF73 dimer dimer, Human herpesvirus 8 protein
Buffer: 25 mM Na/K Phosphate, pH: 7.5
Experiment: SAXS data collected at BM29, ESRF on 2014 Jun 21
KSHV but not MHV-68 LANA induces a strong bend upon binding to terminal repeat viral DNA. Nucleic Acids Res 43(20):10039-54 (2015)
...res de Miranda M, Carrondo MA, Simas JP, Kaye KM, Svergun DI, McVey CE
RgGuinier 2.4 nm
Dmax 9.5 nm
VolumePorod 50 nm3

SASDBD6 – Single stranded poly-deoxythymidine DNA (30mer, dT30)

Poly-deoxythymidine (30mer) experimental SAS data
Single stranded poly-deoxythymidine DNA (30mer, dT30) Rg histogram
Sample: Poly-deoxythymidine (30mer) monomer, DNA
Buffer: 1mM Na MOPS, 20mM NaCl, pH: 7
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2016 Apr 1
...nucleic acids in solution. Nucleic Acids Res 45(9):e66 (2017)
Plumridge A, Meisburger SP, Pollack L
RgGuinier 3.0 nm
Dmax 10.7 nm

SASDBE6 – Single stranded poly-deoxyadenosine DNA (30mer, dA30)

Poly-deoxyadenosine (30mer) experimental SAS data
Single stranded poly-deoxyadenosine DNA (30mer, dA30) Rg histogram
Sample: Poly-deoxyadenosine (30mer) monomer, DNA
Buffer: 1mM Na MOPS, 20mM NaCl, pH: 7
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2015 Apr 1
...nucleic acids in solution. Nucleic Acids Res 45(9):e66 (2017)
Plumridge A, Meisburger SP, Pollack L
RgGuinier 2.7 nm
Dmax 9.5 nm

SASDBG6 – Ribosome biogenesis protein 15 (Nop15)

Ribosome biogenesis protein 15 experimental SAS data
EOM/RANCH model
Sample: Ribosome biogenesis protein 15 monomer, Saccharomyces cerevisiae protein
Buffer: 25 mM HEPES, 500 mM NaCl, 2 mM DTT, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2013 Apr 25
Structural analysis reveals the flexible C-terminus of Nop15 undergoes rearrangement to recognize a pre-ribosomal RNA folding intermediate. Nucleic Acids Res 45(5):2829-2837 (2017)
Zhang J, Gonzalez LE, Hall TMT
RgGuinier 2.4 nm
Dmax 10.3 nm
VolumePorod 38 nm3

SASDAR8 – mLANA 124-316 mLBS1-2 8:1 complex

MHV-68 TR DNALatency-associated nuclear antigen experimental SAS data
CRYSOL model
Sample: MHV-68 TR DNA monomer, unidentified herpesvirus DNA
Latency-associated nuclear antigen octamer, Murid herpesvirus 4 protein
Buffer: 25 mM Na/K Phosphate, pH: 7.5
Experiment: SAXS data collected at P12, PETRA III on 2013 Apr 27
KSHV but not MHV-68 LANA induces a strong bend upon binding to terminal repeat viral DNA. Nucleic Acids Res 43(20):10039-54 (2015)
...res de Miranda M, Carrondo MA, Simas JP, Kaye KM, Svergun DI, McVey CE
RgGuinier 5.8 nm
Dmax 20.0 nm
VolumePorod 475 nm3

SASDBM6 – Nucleolysin TIA-1 isoform p40

Nucleolysin TIA-1 isoform p40 experimental SAS data
Nucleolysin TIA-1 isoform p40 Kratky plot
Sample: Nucleolysin TIA-1 isoform p40 monomer, Homo sapiens protein
Buffer: 20 mM HEPES, 100mM NaCl, 3% v/v glycerol, pH: 7
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 Jul 2
TIA-1 RRM23 binding and recognition of target oligonucleotides. Nucleic Acids Res 45(8):4944-4957 (2017)
Waris S, García-Mauriño SM, Sivakumaran A, Beckham SA, Loughlin FE, Gorospe M, Díaz-Moreno I, Wilce MCJ, Wilce JA
RgGuinier 2.3 nm
Dmax 8.8 nm
VolumePorod 26 nm3

SASDBN6 – Nucleolysin TIA-1 isoform p40 in complex with ACUCCUUUUU RNA

Nucleolysin TIA-1 isoform p40RNA (ACUCCUUUUU) experimental SAS data
Nucleolysin TIA-1 isoform p40 RNA (ACUCCUUUUU) Kratky plot
Sample: Nucleolysin TIA-1 isoform p40 monomer, Homo sapiens protein
RNA (ACUCCUUUUU) monomer, RNA
Buffer: 20 mM HEPES, 100mM NaCl, 3% v/v glycerol, pH: 7
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2016 May 27
TIA-1 RRM23 binding and recognition of target oligonucleotides. Nucleic Acids Res 45(8):4944-4957 (2017)
Waris S, García-Mauriño SM, Sivakumaran A, Beckham SA, Loughlin FE, Gorospe M, Díaz-Moreno I, Wilce MCJ, Wilce JA
RgGuinier 2.2 nm
Dmax 6.6 nm
VolumePorod 30 nm3

SASDBP6 – Nucleolysin TIA-1 isoform p40 in complex with ACTCCTTTTT DNA

Nucleolysin TIA-1 isoform p40DNA (ACTCCTTTTT) experimental SAS data
Nucleolysin TIA-1 isoform p40 DNA (ACTCCTTTTT) Kratky plot
Sample: Nucleolysin TIA-1 isoform p40 monomer, Homo sapiens protein
DNA (ACTCCTTTTT) monomer, DNA
Buffer: 20 mM HEPES, 100mM NaCl, 3% v/v glycerol, pH: 7
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2016 May 27
TIA-1 RRM23 binding and recognition of target oligonucleotides. Nucleic Acids Res 45(8):4944-4957 (2017)
Waris S, García-Mauriño SM, Sivakumaran A, Beckham SA, Loughlin FE, Gorospe M, Díaz-Moreno I, Wilce MCJ, Wilce JA
RgGuinier 2.2 nm
Dmax 6.7 nm
VolumePorod 32 nm3

SASDBQ6 – Nucleolysin TIA-1 isoform p40 in complex with TTTTTACTCC DNA

Nucleolysin TIA-1 isoform p40DNA (TTTTTACTCC) experimental SAS data
Nucleolysin TIA-1 isoform p40 DNA (TTTTTACTCC) Kratky plot
Sample: Nucleolysin TIA-1 isoform p40 monomer, Homo sapiens protein
DNA (TTTTTACTCC) monomer, DNA
Buffer: 20 mM HEPES, 100mM NaCl, 3% v/v glycerol, pH: 7
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2016 May 27
TIA-1 RRM23 binding and recognition of target oligonucleotides. Nucleic Acids Res 45(8):4944-4957 (2017)
Waris S, García-Mauriño SM, Sivakumaran A, Beckham SA, Loughlin FE, Gorospe M, Díaz-Moreno I, Wilce MCJ, Wilce JA
RgGuinier 2.1 nm
Dmax 7.1 nm
VolumePorod 32 nm3

SASDBR6 – Nucleolysin TIA-1 isoform p40 in complex with UUUUUACUCC RNA

Nucleolysin TIA-1 isoform p40RNA (UUUUUACU) experimental SAS data
Nucleolysin TIA-1 isoform p40 RNA (UUUUUACU) Kratky plot
Sample: Nucleolysin TIA-1 isoform p40 monomer, Homo sapiens protein
RNA (UUUUUACU) monomer, RNA
Buffer: 20 mM HEPES, 100mM NaCl, 3% v/v glycerol, pH: 7
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2016 May 27
TIA-1 RRM23 binding and recognition of target oligonucleotides. Nucleic Acids Res 45(8):4944-4957 (2017)
Waris S, García-Mauriño SM, Sivakumaran A, Beckham SA, Loughlin FE, Gorospe M, Díaz-Moreno I, Wilce MCJ, Wilce JA
RgGuinier 2.1 nm
Dmax 6.5 nm
VolumePorod 26 nm3

SASDAP8 – kLBS1-2 DNA

kLBS1-2 DNA experimental SAS data
CRYSOL model
Sample: kLBS1-2 DNA monomer, unidentified herpesvirus DNA
Buffer: Tris, pH: 7.6
Experiment: SAXS data collected at BM29, ESRF on 2013 Apr 27
KSHV but not MHV-68 LANA induces a strong bend upon binding to terminal repeat viral DNA. Nucleic Acids Res 43(20):10039-54 (2015)
...res de Miranda M, Carrondo MA, Simas JP, Kaye KM, Svergun DI, McVey CE
RgGuinier 4.0 nm
Dmax 16.0 nm
VolumePorod 50 nm3

SASDBA7 – Human NEI like DNA glycosylase 1 (NEIL1) bound to Proliferating Cell Nuclear Antigen (PCNA) and DNA

Endonuclease 8-like 1dsDNAProliferating cell nuclear antigen experimental SAS data
DAMMIN model
Sample: Endonuclease 8-like 1 monomer, Homo sapiens protein
dsDNA monomer, DNA
Proliferating cell nuclear antigen monomer, Homo sapiens protein
Buffer: 25mM HEPES 100mM NaCl 1mM DTT, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2016 Jan 20
Destabilization of the PCNA trimer mediated by its interaction with the NEIL1 DNA glycosylase. Nucleic Acids Res 45(5):2897-2909 (2017)
Prakash A, Moharana K, Wallace SS, Doublié S
RgGuinier 3.4 nm
Dmax 16.4 nm
VolumePorod 113 nm3

SASDBB7 – Human NEI like DNA glycosylase 1 (NEIL1) bound to DNA

Endonuclease 8-like 1dsDNA experimental SAS data
DAMMIN model
Sample: Endonuclease 8-like 1 monomer, Homo sapiens protein
dsDNA monomer, DNA
Buffer: 25mM HEPES 100mM NaCl 1mM DTT, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2016 Jan 20
Destabilization of the PCNA trimer mediated by its interaction with the NEIL1 DNA glycosylase. Nucleic Acids Res 45(5):2897-2909 (2017)
Prakash A, Moharana K, Wallace SS, Doublié S
RgGuinier 3.3 nm
Dmax 17.5 nm
VolumePorod 92 nm3

SASDBC7 – Human NEI like DNA glycosylase 1 (NEIL1)

Endonuclease 8-like 1 experimental SAS data
GASBOR model
Sample: Endonuclease 8-like 1 monomer, Homo sapiens protein
Buffer: 25mM HEPES 300mM NaCl 1mM DTT 10% Glycerol, pH: 7.5
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS) on 2015 Mar 13
Destabilization of the PCNA trimer mediated by its interaction with the NEIL1 DNA glycosylase. Nucleic Acids Res 45(5):2897-2909 (2017)
Prakash A, Moharana K, Wallace SS, Doublié S
RgGuinier 3.6 nm
Dmax 15.0 nm
VolumePorod 81 nm3

SASDBD7 – Human Proliferating Cell Nuclear Antigen (PCNA)

Proliferating cell nuclear antigen experimental SAS data
GASBOR model
Sample: Proliferating cell nuclear antigen trimer, Homo sapiens protein
Buffer: 25mM HEPES 100mM NaCl 1mM DTT, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2016 Jan 20
Destabilization of the PCNA trimer mediated by its interaction with the NEIL1 DNA glycosylase. Nucleic Acids Res 45(5):2897-2909 (2017)
Prakash A, Moharana K, Wallace SS, Doublié S
RgGuinier 3.4 nm
Dmax 9.7 nm
VolumePorod 128 nm3

SASDAN3 – MutS dimer

DNA mismatch repair protein MutS experimental SAS data
DAMMIF model
Sample: DNA mismatch repair protein MutS dimer, Escherichia coli protein
Buffer: 50 mM HEPES 50 mM KCl, pH: 7.5
Experiment: SAXS data collected at P12, PETRA III on 2013 Feb 28
Using stable MutS dimers and tetramers to quantitatively analyze DNA mismatch recognition and sliding clamp formation. Nucleic Acids Res 41(17):8166-81 (2013)
Groothuizen FS, Fish A, Petoukhov MV, Reumer A, Manelyte L, Winterwerp HH, Marinus MG, Lebbink JH, Svergun DI, Friedhoff P, Sixma TK
RgGuinier 4.7 nm
Dmax 15.5 nm
VolumePorod 307 nm3

SASDAQ3 – MutS tetramer

DNA mismatch repair protein MutS experimental SAS data
DAMMIF model
Sample: DNA mismatch repair protein MutS tetramer, Escherichia coli protein
Buffer: 50 mM HEPES 50 mM KCl, pH: 7.5
Experiment: SAXS data collected at X33, DORIS III on 2011 May 12
Using stable MutS dimers and tetramers to quantitatively analyze DNA mismatch recognition and sliding clamp formation. Nucleic Acids Res 41(17):8166-81 (2013)
Groothuizen FS, Fish A, Petoukhov MV, Reumer A, Manelyte L, Winterwerp HH, Marinus MG, Lebbink JH, Svergun DI, Friedhoff P, Sixma TK
RgGuinier 7.8 nm
Dmax 28.0 nm
VolumePorod 700 nm3

SASDBX3 – Aureobox dsDNA

Aureobox dsDNA experimental SAS data
DAMFILT model
Sample: Aureobox dsDNA monomer, synthetic construct DNA
Buffer: 50 mM Tris 50 mM boric acid 1 mM EDTA, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2014 Nov 6
...responsive domains of diatom class I aureochromes. Nucleic Acids Res 44(12):5957-70 (2016)
Banerjee A, Herman E, Serif M, Maestre-Reyna M, Hepp S, Pokorny R, Kroth PG, Essen LO, Kottke T
RgGuinier 2.0 nm
Dmax 8.6 nm
VolumePorod 18 nm3

SASDAY3 – MutS tetramer

DNA mismatch repair protein MutS experimental SAS data
DNA mismatch repair protein MutS Kratky plot
Sample: DNA mismatch repair protein MutS tetramer, Escherichia coli protein
Buffer: 50 mM HEPES 50 mM KCl, pH: 7.5
Experiment: SAXS data collected at X33, DORIS III on 2011 May 12
Using stable MutS dimers and tetramers to quantitatively analyze DNA mismatch recognition and sliding clamp formation. Nucleic Acids Res 41(17):8166-81 (2013)
Groothuizen FS, Fish A, Petoukhov MV, Reumer A, Manelyte L, Winterwerp HH, Marinus MG, Lebbink JH, Svergun DI, Friedhoff P, Sixma TK
RgGuinier 8.3 nm
Dmax 29.0 nm
VolumePorod 720 nm3

SASDAZ3 – MutS tetramer

DNA mismatch repair protein MutS experimental SAS data
DNA mismatch repair protein MutS Kratky plot
Sample: DNA mismatch repair protein MutS tetramer, Escherichia coli protein
Buffer: 50 mM HEPES 50 mM KCl, pH: 7.5
Experiment: SAXS data collected at X33, DORIS III on 2011 May 12
Using stable MutS dimers and tetramers to quantitatively analyze DNA mismatch recognition and sliding clamp formation. Nucleic Acids Res 41(17):8166-81 (2013)
Groothuizen FS, Fish A, Petoukhov MV, Reumer A, Manelyte L, Winterwerp HH, Marinus MG, Lebbink JH, Svergun DI, Friedhoff P, Sixma TK
RgGuinier 8.0 nm

SASDA24 – MutS tetramer

DNA mismatch repair protein MutS experimental SAS data
DNA mismatch repair protein MutS Kratky plot
Sample: DNA mismatch repair protein MutS tetramer, Escherichia coli protein
Buffer: 50 mM HEPES 50 mM KCl, pH: 7.5
Experiment: SAXS data collected at X33, DORIS III on 2011 May 12
Using stable MutS dimers and tetramers to quantitatively analyze DNA mismatch recognition and sliding clamp formation. Nucleic Acids Res 41(17):8166-81 (2013)
Groothuizen FS, Fish A, Petoukhov MV, Reumer A, Manelyte L, Winterwerp HH, Marinus MG, Lebbink JH, Svergun DI, Friedhoff P, Sixma TK
RgGuinier 7.8 nm
Dmax 27.0 nm

SASDB34 – Aureochrome 1a bZIP-LOV module: PtAUREO1a bZIP-LOV (Light oxygen voltage) module (dark state, Tris)

Aureochrome 1a bZIP-LOV module experimental SAS data
Aureochrome 1a bZIP-LOV module Kratky plot
Sample: Aureochrome 1a bZIP-LOV module dimer, Phaeodactylum tricornutum protein
Buffer: 10 mM Tris 300 mM NaCl, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2014 Nov 6
...responsive domains of diatom class I aureochromes. Nucleic Acids Res 44(12):5957-70 (2016)
Banerjee A, Herman E, Serif M, Maestre-Reyna M, Hepp S, Pokorny R, Kroth PG, Essen LO, Kottke T
RgGuinier 3.8 nm
Dmax 12.5 nm
VolumePorod 117 nm3

SASDB48 – Major viral transcription factor ICP4/Immediate Early 3 DNA (ICP4N IE3_19mer) complex

Major viral transcription factor ICP4Immediate Early 3 experimental SAS data
NONE model
Sample: Major viral transcription factor ICP4 dimer, Human herpesvirus 1 ... protein
Immediate Early 3 dimer, DNA
Buffer: 20 mM HEPES, 150 mM NaCl, pH: 7.4
Experiment: SAXS data collected at B21, Diamond Light Source on 2015 Jul 27
The herpes viral transcription factor ICP4 forms a novel DNA recognition complex. Nucleic Acids Res 45(13):8064-8078 (2017)
Tunnicliffe RB, Lockhart-Cairns MP, Levy C, Mould AP, Jowitt TA, Sito H, Baldock C, Sandri-Goldin RM, Golovanov AP
RgGuinier 2.5 nm
Dmax 8.3 nm
VolumePorod 90 nm3

SASDB58 – Major viral transcription factor ICP4 (ICP4N dimer)

Major viral transcription factor ICP4 experimental SAS data
Major viral transcription factor ICP4 Kratky plot
Sample: Major viral transcription factor ICP4 dimer, Human herpesvirus 1 ... protein
Buffer: 20 mM HEPES, 150 mM NaCl, pH: 7.4
Experiment: SAXS data collected at B21, Diamond Light Source on 2015 Jul 27
The herpes viral transcription factor ICP4 forms a novel DNA recognition complex. Nucleic Acids Res 45(13):8064-8078 (2017)
Tunnicliffe RB, Lockhart-Cairns MP, Levy C, Mould AP, Jowitt TA, Sito H, Baldock C, Sandri-Goldin RM, Golovanov AP
RgGuinier 2.9 nm
Dmax 12.7 nm

SASDB68 – Immediate Early 3 DNA (ICP4N IE3_19mer)

Immediate Early 3 experimental SAS data
Immediate Early 3 Kratky plot
Sample: Immediate Early 3 dimer, DNA
Buffer: 20 mM HEPES, 150 mM NaCl, pH: 7.4
Experiment: SAXS data collected at BM29, ESRF on 2015 Nov 12
The herpes viral transcription factor ICP4 forms a novel DNA recognition complex. Nucleic Acids Res 45(13):8064-8078 (2017)
Tunnicliffe RB, Lockhart-Cairns MP, Levy C, Mould AP, Jowitt TA, Sito H, Baldock C, Sandri-Goldin RM, Golovanov AP
RgGuinier 1.9 nm
Dmax 6.9 nm

SASDB78 – Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I)

Probable ATP-dependent RNA helicase DDX58 experimental SAS data
BUNCH model
Sample: Probable ATP-dependent RNA helicase DDX58 monomer, Homo sapiens protein
Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, pH: 7.4
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2012 Apr 6
Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis. Nucleic Acids Res (2018)
Shah N, Beckham SA, Wilce JA, Wilce MCJ
RgGuinier 4.3 nm
Dmax 14.0 nm
VolumePorod 186 nm3

SASDB88 – Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) plus ADP-AlFx

Probable ATP-dependent RNA helicase DDX58 experimental SAS data
EOM/RANCH model
Sample: Probable ATP-dependent RNA helicase DDX58 monomer, Homo sapiens protein
Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 2mM ADP-AlFx, pH: 7.4
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 Nov 20
Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis. Nucleic Acids Res (2018)
Shah N, Beckham SA, Wilce JA, Wilce MCJ
RgGuinier 4.2 nm
Dmax 15.6 nm
VolumePorod 190 nm3

SASDB98 – Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) plus bound 10mer hairpin dsRNA

Probable ATP-dependent RNA helicase DDX585´ppp 10mer hairpin dsRNA experimental SAS data
EOM/RANCH model
Sample: Probable ATP-dependent RNA helicase DDX58 monomer, Homo sapiens protein
5´ppp 10mer hairpin dsRNA monomer, RNA
Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, pH: 7.4
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 May 29
Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis. Nucleic Acids Res (2018)
Shah N, Beckham SA, Wilce JA, Wilce MCJ
RgGuinier 4.1 nm
Dmax 16.1 nm
VolumePorod 160 nm3

SASDBA8 – Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) plus 10mer hairpin dsRNA /AMP-PNP

Probable ATP-dependent RNA helicase DDX585´ppp 10mer hairpin dsRNA experimental SAS data
EOM/RANCH model
Sample: Probable ATP-dependent RNA helicase DDX58 monomer, Homo sapiens protein
5´ppp 10mer hairpin dsRNA monomer, RNA
Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 0.5 mM AMP-PNP, pH: 7.4
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 May 28
Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis. Nucleic Acids Res (2018)
Shah N, Beckham SA, Wilce JA, Wilce MCJ
RgGuinier 4.2 nm
Dmax 17.0 nm
VolumePorod 163 nm3

SASDBB8 – Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) plus 10mer hairpin dsRNA and ADP-AlFx

Probable ATP-dependent RNA helicase DDX585´ppp 10mer hairpin dsRNA experimental SAS data
EOM/RANCH model
Sample: Probable ATP-dependent RNA helicase DDX58 monomer, Homo sapiens protein
5´ppp 10mer hairpin dsRNA monomer, RNA
Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 2mM ADP-AlFx, pH: 7.4
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 Nov 20
Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis. Nucleic Acids Res (2018)
Shah N, Beckham SA, Wilce JA, Wilce MCJ
RgGuinier 4.0 nm
Dmax 18.3 nm
VolumePorod 156 nm3

SASDBD8 – Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) plus 8mer hairpin dsRNA (SEC-peak1)

Probable ATP-dependent RNA helicase DDX585´ppp 8mer hairpin dsRNA experimental SAS data
EOM/RANCH model
Sample: Probable ATP-dependent RNA helicase DDX58 monomer, Homo sapiens protein
5´ppp 8mer hairpin dsRNA monomer, RNA
Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, pH: 7.4
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 Nov 20
Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis. Nucleic Acids Res (2018)
Shah N, Beckham SA, Wilce JA, Wilce MCJ
RgGuinier 4.3 nm
Dmax 15.3 nm
VolumePorod 179 nm3

SASDBE8 – Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) 8mer hairpin dsRNA/AMP-PNP (SEC-peak1)

Probable ATP-dependent RNA helicase DDX585´ppp 8mer hairpin dsRNA experimental SAS data
EOM/RANCH model
Sample: Probable ATP-dependent RNA helicase DDX58 monomer, Homo sapiens protein
5´ppp 8mer hairpin dsRNA monomer, RNA
Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 0.5 mM AMP-PNP, pH: 7.4
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2016 Apr 27
Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis. Nucleic Acids Res (2018)
Shah N, Beckham SA, Wilce JA, Wilce MCJ
RgGuinier 4.1 nm
Dmax 15.0 nm
VolumePorod 188 nm3

SASDBF8 – Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) 8mer hairpin dsRNA/ADP-AlFx (SECpeak1)

Probable ATP-dependent RNA helicase DDX585´ppp 8mer hairpin dsRNA experimental SAS data
EOM/RANCH model
Sample: Probable ATP-dependent RNA helicase DDX58 monomer, Homo sapiens protein
5´ppp 8mer hairpin dsRNA monomer, RNA
Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 2mM ADP-AlFx, pH: 7.4
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 Nov 20
Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis. Nucleic Acids Res (2018)
Shah N, Beckham SA, Wilce JA, Wilce MCJ
RgGuinier 4.2 nm
Dmax 16.8 nm
VolumePorod 178 nm3

SASDBG8 – Probable ATP-dependent RNA helicase DDX58 without CARDs (Delta-CARDs RIG-I)

Probable ATP-dependent RNA helicase DDX58 (without CARDs) experimental SAS data
BUNCH model
Sample: Probable ATP-dependent RNA helicase DDX58 (without CARDs) monomer, Homo sapiens protein
Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, pH: 7.4
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 May 29
Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis. Nucleic Acids Res (2018)
Shah N, Beckham SA, Wilce JA, Wilce MCJ
RgGuinier 3.7 nm
Dmax 13.0 nm
VolumePorod 114 nm3

SASDBH8 – Probable ATP-dependent RNA helicase DDX58 without CARDs (Delta-CARDs RIG-I) plus ADP-AlFx

Probable ATP-dependent RNA helicase DDX58 (without CARDs) experimental SAS data
EOM/RANCH model
Sample: Probable ATP-dependent RNA helicase DDX58 (without CARDs) monomer, Homo sapiens protein
Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 2mM ADP-AlFx, pH: 7.4
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 Nov 20
Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis. Nucleic Acids Res (2018)
Shah N, Beckham SA, Wilce JA, Wilce MCJ
RgGuinier 3.5 nm
Dmax 14.0 nm
VolumePorod 132 nm3

SASDBJ8 – Probable ATP-dependent RNA helicase DDX58 without CARDs (Delta-CARDs RIG-I) plus 10mer hairpin dsRNA

Probable ATP-dependent RNA helicase DDX58 (without CARDs)5´ppp 10mer hairpin dsRNA experimental SAS data
CORAL model
Sample: Probable ATP-dependent RNA helicase DDX58 (without CARDs) monomer, Homo sapiens protein
5´ppp 10mer hairpin dsRNA monomer, RNA
Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, pH: 7.4
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 May 29
Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis. Nucleic Acids Res (2018)
Shah N, Beckham SA, Wilce JA, Wilce MCJ
RgGuinier 2.8 nm
Dmax 9.0 nm
VolumePorod 146 nm3

SASDBK8 – Probable ATP-dependent RNA helicase DDX58 (Delta-CARDs RIG-I) plus 10mer hairpin dsRNA and AMP-PNP

Probable ATP-dependent RNA helicase DDX58 (without CARDs)5´ppp 10mer hairpin dsRNA experimental SAS data
CORAL model
Sample: Probable ATP-dependent RNA helicase DDX58 (without CARDs) monomer, Homo sapiens protein
5´ppp 10mer hairpin dsRNA monomer, RNA
Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 0.5 mM AMP-PNP, pH: 7.4
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 May 29
Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis. Nucleic Acids Res (2018)
Shah N, Beckham SA, Wilce JA, Wilce MCJ
RgGuinier 2.8 nm
Dmax 9.0 nm
VolumePorod 135 nm3

SASDBL8 – Probable ATP-dependent RNA helicase DDX58 (Delta-CARDs RIG-I) plus 10mer hairpin dsRNA and ADP-AlFx

Probable ATP-dependent RNA helicase DDX58 (without CARDs)5´ppp 10mer hairpin dsRNA experimental SAS data
CORAL model
Sample: Probable ATP-dependent RNA helicase DDX58 (without CARDs) monomer, Homo sapiens protein
5´ppp 10mer hairpin dsRNA monomer, RNA
Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 2mM ADP-AlFx, pH: 7.4
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 Nov 20
Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis. Nucleic Acids Res (2018)
Shah N, Beckham SA, Wilce JA, Wilce MCJ
RgGuinier 2.8 nm
Dmax 8.9 nm
VolumePorod 137 nm3

SASDBM8 – Probable ATP-dependent RNA helicase DDX58 (Delta-CARDs RIG-I) plus 8mer hairpin dsRNA (SEC-peak1)

Probable ATP-dependent RNA helicase DDX58 (without CARDs)5´ppp 8mer hairpin dsRNA experimental SAS data
EOM/RANCH model
Sample: Probable ATP-dependent RNA helicase DDX58 (without CARDs) monomer, Homo sapiens protein
5´ppp 8mer hairpin dsRNA monomer, RNA
Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, pH: 7.4
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 May 29
Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis. Nucleic Acids Res (2018)
Shah N, Beckham SA, Wilce JA, Wilce MCJ
RgGuinier 3.4 nm
Dmax 11.6 nm
VolumePorod 132 nm3

SASDBN8 – Probable ATP-dependent RNA helicase DDX58 (Delta-CARDs) plus 8mer hairpin dsRNA/AMP-PNP (SEC-peak1)

Probable ATP-dependent RNA helicase DDX58 (without CARDs)5´ppp 8mer hairpin dsRNA experimental SAS data
EOM/RANCH model
Sample: Probable ATP-dependent RNA helicase DDX58 (without CARDs) monomer, Homo sapiens protein
5´ppp 8mer hairpin dsRNA monomer, RNA
Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 0.5 mM AMP-PNP, pH: 7.4
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2016 Apr 27
Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis. Nucleic Acids Res (2018)
Shah N, Beckham SA, Wilce JA, Wilce MCJ
RgGuinier 3.2 nm
Dmax 11.1 nm
VolumePorod 114 nm3

SASDBP8 – Probable ATP-dependent RNA helicase DDX58 (Delta-CARDs) plus 8mer hairpin dsRNA/ADP-AlFx (SEC-peak1)

Probable ATP-dependent RNA helicase DDX58 (without CARDs)5´ppp 8mer hairpin dsRNA experimental SAS data
CORAL model
Sample: Probable ATP-dependent RNA helicase DDX58 (without CARDs) monomer, Homo sapiens protein
5´ppp 8mer hairpin dsRNA monomer, RNA
Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 2mM ADP-AlFx, pH: 7.4
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 Nov 20
Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis. Nucleic Acids Res (2018)
Shah N, Beckham SA, Wilce JA, Wilce MCJ
RgGuinier 3.0 nm
Dmax 10.5 nm
VolumePorod 132 nm3

SASDBQ8 – Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) plus 8mer hairpin dsRNA (SEC-peak2)

Probable ATP-dependent RNA helicase DDX585´ppp 8mer hairpin dsRNA experimental SAS data
Probable ATP-dependent RNA helicase DDX58 5´ppp 8mer hairpin dsRNA Kratky plot
Sample: Probable ATP-dependent RNA helicase DDX58 dimer, Homo sapiens protein
5´ppp 8mer hairpin dsRNA dimer, RNA
Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, pH: 7.4
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 Nov 20
Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis. Nucleic Acids Res (2018)
Shah N, Beckham SA, Wilce JA, Wilce MCJ
RgGuinier 5.7 nm
Dmax 24.6 nm
VolumePorod 389 nm3

SASDBR8 – Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I), 8mer hairpin dsRNA/AMP-PNP (SECpeak2)

Probable ATP-dependent RNA helicase DDX585´ppp 8mer hairpin dsRNA experimental SAS data
Probable ATP-dependent RNA helicase DDX58 5´ppp 8mer hairpin dsRNA Kratky plot
Sample: Probable ATP-dependent RNA helicase DDX58 dimer, Homo sapiens protein
5´ppp 8mer hairpin dsRNA dimer, RNA
Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 0.5 mM AMP-PNP, pH: 7.4
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2016 Apr 27
Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis. Nucleic Acids Res (2018)
Shah N, Beckham SA, Wilce JA, Wilce MCJ
RgGuinier 5.8 nm
Dmax 24.6 nm
VolumePorod 450 nm3

SASDBS8 – Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) 8mer hairpin dsRNA/ADP-AlFx (SECpeak2)

Probable ATP-dependent RNA helicase DDX585´ppp 8mer hairpin dsRNA experimental SAS data
Probable ATP-dependent RNA helicase DDX58 5´ppp 8mer hairpin dsRNA Kratky plot
Sample: Probable ATP-dependent RNA helicase DDX58 dimer, Homo sapiens protein
5´ppp 8mer hairpin dsRNA dimer, RNA
Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 2mM ADP-AlFx, pH: 7.4
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 Nov 20
Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis. Nucleic Acids Res (2018)
Shah N, Beckham SA, Wilce JA, Wilce MCJ
RgGuinier 5.3 nm
Dmax 25.1 nm
VolumePorod 298 nm3

SASDBT8 – Probable ATP-dependent RNA helicase DDX58 (Delta-CARDs RIG-I) plus 8mer hairpin dsRNA (SEC-peak2)

5´ppp 8mer hairpin dsRNAProbable ATP-dependent RNA helicase DDX58 (without CARDs) experimental SAS data
5´ppp 8mer hairpin dsRNA Probable ATP-dependent RNA helicase DDX58 (without CARDs) Kratky plot
Sample: 5´ppp 8mer hairpin dsRNA dimer, RNA
Probable ATP-dependent RNA helicase DDX58 (without CARDs) dimer, Homo sapiens protein
Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, pH: 7.4
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 May 29
Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis. Nucleic Acids Res (2018)
Shah N, Beckham SA, Wilce JA, Wilce MCJ
RgGuinier 4.1 nm
Dmax 15.0 nm
VolumePorod 273 nm3

SASDBU8 – Probable ATP-dependent RNA helicase DDX58 (Delta-CARDs) plus 8mer hairpin dsRNA/AMP-PNP (SEC-peak2)

5´ppp 8mer hairpin dsRNAProbable ATP-dependent RNA helicase DDX58 (without CARDs) experimental SAS data
5´ppp 8mer hairpin dsRNA Probable ATP-dependent RNA helicase DDX58 (without CARDs) Kratky plot
Sample: 5´ppp 8mer hairpin dsRNA dimer, RNA
Probable ATP-dependent RNA helicase DDX58 (without CARDs) dimer, Homo sapiens protein
Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 0.5 mM AMP-PNP, pH: 7.4
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2016 Apr 27
Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis. Nucleic Acids Res (2018)
Shah N, Beckham SA, Wilce JA, Wilce MCJ
RgGuinier 3.8 nm
Dmax 15.4 nm
VolumePorod 226 nm3

SASDBV8 – Probable ATP-dependent RNA helicase DDX58 (Delta-CARDs) plus 8mer hairpin dsRNA/ADP-AlFx (SEC-peak2)

5´ppp 8mer hairpin dsRNAProbable ATP-dependent RNA helicase DDX58 (without CARDs) experimental SAS data
SASREF model
Sample: 5´ppp 8mer hairpin dsRNA dimer, RNA
Probable ATP-dependent RNA helicase DDX58 (without CARDs) dimer, Homo sapiens protein
Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 2mM ADP-AlFx, pH: 7.4
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 Nov 20
Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis. Nucleic Acids Res (2018)
Shah N, Beckham SA, Wilce JA, Wilce MCJ
RgGuinier 3.9 nm
Dmax 16.0 nm
VolumePorod 230 nm3

SASDCY4 – RNase E 603-850

RNase E 603-850 experimental SAS data
RNase E 603-850 Rg histogram
Sample: RNase E 603-850 monomer, Escherichia coli protein
Buffer: 50 mM Tris HCl, 100 mM NaCl, 100 mM KCl, 10 mM MgCl2, 10 mM DTT and 5 % glycerol (v/v), pH: 7.5
Experiment: SAXS data collected at SWING, SOLEIL on 2014 Dec 5
Analysis of the natively unstructured RNA/protein-recognition core in the Escherichia coli RNA degradosome and its interactions with regulatory RNA/Hfq complexes. Nucleic Acids Res 46(1):387-402 (2018)
Bruce HA, Du D, Matak-Vinkovic D, Bandyra KJ, Broadhurst RW, Martin E, Sobott F, Shkumatov AV, Luisi BF
RgGuinier 5.3 nm
Dmax 27.5 nm
VolumePorod 139 nm3

SASDBZ8 – Single stranded poly-deoxyadenosine DNA (30mer, dA30) in 100 mM NaCl

Poly-deoxyadenosine (30mer) experimental SAS data
CUSTOM IN-HOUSE model
Sample: Poly-deoxyadenosine (30mer) monomer, DNA
Buffer: 1mM Na MOPS, 100mM NaCl, pH: 7
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2015 Apr 1
The impact of base stacking on the conformations and electrostatics of single-stranded DNA. Nucleic Acids Res 45(7):3932-3943 (2017)
...resen K, Pollack L
RgGuinier 2.7 nm
Dmax 10.0 nm
VolumePorod 16 nm3

SASDB29 – Single stranded poly-deoxyadenosine DNA (30mer, dA30) in 200 mM NaCl

Poly-deoxyadenosine (30mer) experimental SAS data
CUSTOM IN-HOUSE model
Sample: Poly-deoxyadenosine (30mer) monomer, DNA
Buffer: 1mM Na MOPS, 200mM NaCl, pH: 7
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2015 Apr 1
The impact of base stacking on the conformations and electrostatics of single-stranded DNA. Nucleic Acids Res 45(7):3932-3943 (2017)
...resen K, Pollack L
RgGuinier 2.7 nm
Dmax 9.5 nm
VolumePorod 15 nm3

SASDB39 – Single stranded poly-deoxythymidine DNA (30mer, dT30) in 100 mM NaCl

Poly-deoxythymidine (30mer) experimental SAS data
CUSTOM IN-HOUSE model
Sample: Poly-deoxythymidine (30mer) monomer, DNA
Buffer: 1mM Na MOPS, 100mM NaCl, pH: 7
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2015 Apr 1
The impact of base stacking on the conformations and electrostatics of single-stranded DNA. Nucleic Acids Res 45(7):3932-3943 (2017)
...resen K, Pollack L
RgGuinier 2.8 nm

SASDB49 – Single stranded poly-deoxythymidine DNA (30mer, dT30) in 200 mM NaCl

Poly-deoxythymidine (30mer) experimental SAS data
CUSTOM IN-HOUSE model
Sample: Poly-deoxythymidine (30mer) monomer, DNA
Buffer: 1mM Na MOPS, 200mM NaCl, pH: 7
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2015 Apr 1
The impact of base stacking on the conformations and electrostatics of single-stranded DNA. Nucleic Acids Res 45(7):3932-3943 (2017)
...resen K, Pollack L
RgGuinier 2.7 nm

SASDAM8 – MHV-68 LANA

Latency-associated nuclear antigen experimental SAS data
MHV-68 LANA Rg histogram
Sample: Latency-associated nuclear antigen tetramer, Murid herpesvirus 4 protein
Buffer: 25 mM Na/K Phosphate, pH: 7.5
Experiment: SAXS data collected at P12, PETRA III on 2013 Apr 27
KSHV but not MHV-68 LANA induces a strong bend upon binding to terminal repeat viral DNA. Nucleic Acids Res 43(20):10039-54 (2015)
...res de Miranda M, Carrondo MA, Simas JP, Kaye KM, Svergun DI, McVey CE
RgGuinier 4.2 nm
Dmax 16.0 nm
VolumePorod 117 nm3

SASDCZ4 – RNase E 603-850/ATP-dependent RNA helicase (RhlB) binary complex

RNase E 603-850ATP-dependent RNA helicase RhlB experimental SAS data
GASBOR model
Sample: RNase E 603-850 monomer, Escherichia coli protein
ATP-dependent RNA helicase RhlB monomer, Escherichia coli protein
Buffer: 50 mM Tris HCl, 100 mM NaCl, 100 mM KCl, 10 mM MgCl2, 10 mM DTT and 5 % glycerol (v/v), pH: 7.5
Experiment: SAXS data collected at SWING, SOLEIL on 2016 Feb 11
Analysis of the natively unstructured RNA/protein-recognition core in the Escherichia coli RNA degradosome and its interactions with regulatory RNA/Hfq complexes. Nucleic Acids Res 46(1):387-402 (2018)
Bruce HA, Du D, Matak-Vinkovic D, Bandyra KJ, Broadhurst RW, Martin E, Sobott F, Shkumatov AV, Luisi BF
RgGuinier 5.4 nm
Dmax 29.5 nm
VolumePorod 183 nm3

SASDB79 – Basic domain of human telomeric repeat-binding factor 2 (TRF2) in complex with telomeric DNA duplex

Basic domain of telomeric repeat-binding factor 2telomere DNA duplex experimental SAS data
MONSA model
Sample: Basic domain of telomeric repeat-binding factor 2 monomer, Homo sapiens protein
telomere DNA duplex monomer, DNA
Buffer: 20 mM Tris-HCl, 50 mM LiCl, pH: 7.5
Experiment: SAXS data collected at Rigaku BioSAXS-1000, CEITEC on 2016 May 3
...restores it. Nucleic Acids Res 45(21):12170-12180 (2017)
Necasová I, Janoušková E, Klumpler T, Hofr C
RgGuinier 1.7 nm
Dmax 6.0 nm
VolumePorod 20 nm3

SASDB89 – Telomeric DNA duplex

telomere DNA duplex experimental SAS data
MONSA model
Sample: telomere DNA duplex monomer, DNA
Buffer: 20 mM Tris-HCl, 50 mM LiCl, pH: 7.5
Experiment: SAXS data collected at Rigaku BioSAXS-1000, CEITEC on 2016 May 3
...restores it. Nucleic Acids Res 45(21):12170-12180 (2017)
Necasová I, Janoušková E, Klumpler T, Hofr C
RgGuinier 1.6 nm
Dmax 5.7 nm
VolumePorod 12 nm3

SASDBA9 – E. coli CcdB2-CcdA2-CcdB2 toxin/antitoxin heterohexamer complex

Toxin CcdBAntitoxin CcdAToxin CcdB experimental SAS data
MODELLER model
Sample: Toxin CcdB dimer, Escherichia coli (strain ... protein
Antitoxin CcdA dimer, Escherichia coli (strain ... protein
Toxin CcdB dimer, Escherichia coli (strain ... protein
Buffer: 10 mM Tris 50 mM NaCl, pH: 7.3
Experiment: SAXS data collected at SWING, SOLEIL on 2013 Jul 24
Molecular mechanism governing ratio-dependent transcription regulation in the ccdAB operon. Nucleic Acids Res 45(6):2937-2950 (2017)
Vandervelde A, Drobnak I, Hadži S, Sterckx YG, Welte T, De Greve H, Charlier D, Efremov R, Loris R, Lah J
RgGuinier 3.4 nm
Dmax 12.0 nm
VolumePorod 92 nm3

SASDBK4 – The 1:1:3:1 crRNA:Cas6f:Cas7fv:Cas5fv CRISPR/Cas Type I-F short Cascade complex

short-crRNA: CRISPR/Cas Type I-F Cascade componentCas6f: CRISPR/Cas Type I-F Cascade component (CRISPR-associated protein, Csy4 family)Trimeric Cas7fv: CRISPR/Cas Type I-F Cascade component (Uncharacterized protein, Sputcn32_1821)Cas5fv: CRISPR/Cas Type I-F Cascade component (Uncharacterized protein, Sputcn32_1822) experimental SAS data
DAMMIF model
Sample: short-crRNA: CRISPR/Cas Type I-F Cascade component monomer, Shewanella putrefaciens RNA
Cas6f: CRISPR/Cas Type I-F Cascade component (CRISPR-associated protein, Csy4 family) monomer, Shewanella putrefaciens protein
Trimeric Cas7fv: CRISPR/Cas Type I-F Cascade component (Uncharacterized protein, Sputcn32_1821) trimer, Shewanella putrefaciens protein
Cas5fv: CRISPR/Cas Type I-F Cascade component (Uncharacterized protein, Sputcn32_1822) monomer, Shewanella putrefaciens protein
Buffer: 50 mM HEPES 150 mM NaCl 1mM DTT 1mM EDTA, pH: 7
Experiment: SAXS data collected at BM29, ESRF on 2015 Jun 27
Modulating the Cascade architecture of a minimal Type I-F CRISPR-Cas system. Nucleic Acids Res 44(12):5872-82 (2016)
Gleditzsch D, Müller-Esparza H, Pausch P, Sharma K, Dwarakanath S, Urlaub H, Bange G, Randau L
RgGuinier 4.1 nm
Dmax 14.2 nm

SASDAG5 – RNA shaperone Hfq

RNA chaperone Hfq experimental SAS data
DAMMIN model
Sample: RNA chaperone Hfq hexamer, Escherichia coli protein
Buffer: 50 mM Tris-HCL 150 mM NaCl 1.0 mM DTT, pH: 7.5
Experiment: SAXS data collected at X33, DORIS III on 2008 May 2
Structural insights into the dynamics and function of the C-terminus of the E. coli RNA chaperone Hfq. Nucleic Acids Res 39(11):4900-15 (2011)
Beich-Frandsen M, Vecerek B, Konarev PV, Sjöblom B, Kloiber K, Hämmerle H, Rajkowitsch L, Miles AJ, Kontaxis G, Wallace BA, Svergun DI, Konrat R, Bläsi U, Djinovic-Carugo K
RgGuinier 3.2 nm
Dmax 11.2 nm
VolumePorod 110 nm3

SASDAH5 – Complex of Hfq with DsrA

RNA chaperone HfqRNA DsrA experimental SAS data
SASREF model
Sample: RNA chaperone Hfq hexamer, Escherichia coli protein
RNA DsrA monomer, RNA
Buffer: 50 mM Tris-HCL 150 mM NaCl 1.0 mM DTT, pH: 7.5
Experiment: SAXS data collected at X33, DORIS III on 2010 Nov 16
Structural flexibility of RNA as molecular basis for Hfq chaperone function. Nucleic Acids Res 40(16):8072-84 (2012)
Ribeiro Ede A Jr, Beich-Frandsen M, Konarev PV, Shang W, Vecerek B, Kontaxis G, Hämmerle H, Peterlik H, Svergun DI, Bläsi U, Djinović-Carugo K
RgGuinier 4.3 nm
Dmax 14.5 nm
VolumePorod 210 nm3

SASDBL4 – The 1:1:6:1 crRNA:Cas6f:Cas7fv:Cas5fv CRISPR/Cas Type I-F wild-type Cascade complex

Cas6f: CRISPR/Cas Type I-F Cascade component (CRISPR-associated protein, Csy4 family)Cas5fv: CRISPR/Cas Type I-F Cascade component (Uncharacterized protein, Sputcn32_1822)Hexameric Cas7fv: CRISPR/Cas Type I-F Cascade component (Uncharacterized protein, Sputcn32_1821)wildtype-crRNA: CRISPR/Cas Type I-F Cascade component experimental SAS data
DAMMIF model
Sample: Cas6f: CRISPR/Cas Type I-F Cascade component (CRISPR-associated protein, Csy4 family) monomer, Shewanella putrefaciens protein
Cas5fv: CRISPR/Cas Type I-F Cascade component (Uncharacterized protein, Sputcn32_1822) monomer, Shewanella putrefaciens protein
Hexameric Cas7fv: CRISPR/Cas Type I-F Cascade component (Uncharacterized protein, Sputcn32_1821) hexamer, Shewanella putrefaciens protein
wildtype-crRNA: CRISPR/Cas Type I-F Cascade component monomer, RNA
Buffer: 50 mM HEPES 150 mM NaCl 1mM DTT 1mM EDTA, pH: 7
Experiment: SAXS data collected at BM29, ESRF on 2015 Jun 27
Modulating the Cascade architecture of a minimal Type I-F CRISPR-Cas system. Nucleic Acids Res 44(12):5872-82 (2016)
Gleditzsch D, Müller-Esparza H, Pausch P, Sharma K, Dwarakanath S, Urlaub H, Bange G, Randau L
RgGuinier 5.4 nm
Dmax 18.4 nm

SASDAX3 – MutS tetramer

DNA mismatch repair protein MutS experimental SAS data
DNA mismatch repair protein MutS Kratky plot
Sample: DNA mismatch repair protein MutS tetramer, Escherichia coli protein
Buffer: 50 mM HEPES 50 mM KCl, pH: 7.5
Experiment: SAXS data collected at X33, DORIS III on 2011 May 12
Using stable MutS dimers and tetramers to quantitatively analyze DNA mismatch recognition and sliding clamp formation. Nucleic Acids Res 41(17):8166-81 (2013)
Groothuizen FS, Fish A, Petoukhov MV, Reumer A, Manelyte L, Winterwerp HH, Marinus MG, Lebbink JH, Svergun DI, Friedhoff P, Sixma TK
RgGuinier 8.5 nm
Dmax 29.0 nm
VolumePorod 750 nm3

SASDC25 – RNase E 603-850/ATP-dependent RNA helicase (RhlB)/enolase ternary complex

RNase E 603-850ATP-dependent RNA helicase RhlBEnolase experimental SAS data
GASBOR model
Sample: RNase E 603-850 monomer, Escherichia coli protein
ATP-dependent RNA helicase RhlB monomer, Escherichia coli protein
Enolase dimer, Escherichia coli protein
Buffer: 50 mM Tris HCl, 100 mM NaCl, 100 mM KCl, 10 mM MgCl2, 10 mM DTT and 5 % glycerol (v/v), pH: 7.5
Experiment: SAXS data collected at SWING, SOLEIL on 2014 Jul 16
Analysis of the natively unstructured RNA/protein-recognition core in the Escherichia coli RNA degradosome and its interactions with regulatory RNA/Hfq complexes. Nucleic Acids Res 46(1):387-402 (2018)
Bruce HA, Du D, Matak-Vinkovic D, Bandyra KJ, Broadhurst RW, Martin E, Sobott F, Shkumatov AV, Luisi BF
RgGuinier 6.4 nm
Dmax 30.5 nm
VolumePorod 280 nm3

SASDBM4 – The 1:1:9:1 crRNA:Cas6f:Cas7fv:Cas5fv CRISPR/Cas Type I-F long Cascade complex

Cas6f: CRISPR/Cas Type I-F Cascade component (CRISPR-associated protein, Csy4 family)Cas5fv: CRISPR/Cas Type I-F Cascade component (Uncharacterized protein, Sputcn32_1822)Nonameric Cas7fv: CRISPR/Cas Type I-F Cascade component (Uncharacterized protein, Sputcn32_1821)long-crRNA: CRISPR/Cas Type I-F Cascade component experimental SAS data
DAMMIF model
Sample: Cas6f: CRISPR/Cas Type I-F Cascade component (CRISPR-associated protein, Csy4 family) monomer, Shewanella putrefaciens protein
Cas5fv: CRISPR/Cas Type I-F Cascade component (Uncharacterized protein, Sputcn32_1822) monomer, Shewanella putrefaciens protein
Nonameric Cas7fv: CRISPR/Cas Type I-F Cascade component (Uncharacterized protein, Sputcn32_1821) nonamer, Shewanella putrefaciens protein
long-crRNA: CRISPR/Cas Type I-F Cascade component monomer, RNA
Buffer: 50 mM HEPES 150 mM NaCl 1mM DTT 1mM EDTA, pH: 7
Experiment: SAXS data collected at BM29, ESRF on 2016 Jan 30
Modulating the Cascade architecture of a minimal Type I-F CRISPR-Cas system. Nucleic Acids Res 44(12):5872-82 (2016)
Gleditzsch D, Müller-Esparza H, Pausch P, Sharma K, Dwarakanath S, Urlaub H, Bange G, Randau L
RgGuinier 6.5 nm
Dmax 21.6 nm

SASDAS8 – kLANA 1008-1150 -- kLBS1-2 complex 8:2 (partially dissociated)

kLBS1-2 DNAORF73 tetramerORF73 octamerkLBS1-2 DNA two monomers experimental SAS data
NONE model
Sample: kLBS1-2 DNA monomer, unidentified herpesvirus DNA
ORF73 tetramer tetramer, Human herpesvirus 8 protein
ORF73 octamer octamer, Human herpesvirus 8 protein
kLBS1-2 DNA two monomers dimer, unidentified herpesvirus RNA
Buffer: 25 mM Na/K Phosphate, pH: 7.5
Experiment: SAXS data collected at P12, PETRA III on 2013 Apr 27
KSHV but not MHV-68 LANA induces a strong bend upon binding to terminal repeat viral DNA. Nucleic Acids Res 43(20):10039-54 (2015)
...res de Miranda M, Carrondo MA, Simas JP, Kaye KM, Svergun DI, McVey CE
RgGuinier 4.8 nm
Dmax 16.0 nm
VolumePorod 250 nm3

SASDBY3 – Aureochrome 1a bZIP-LOV module: PtAUREO1a bZIP-LOV (Light oxygen voltage) module (light state-TBE)

Aureochrome 1a bZIP-LOV module experimental SAS data
DAMFILT model
Sample: Aureochrome 1a bZIP-LOV module dimer, Phaeodactylum tricornutum protein
Buffer: 50 mM Tris 50 mM boric acid 1 mM EDTA, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2014 Nov 6
...responsive domains of diatom class I aureochromes. Nucleic Acids Res 44(12):5957-70 (2016)
Banerjee A, Herman E, Serif M, Maestre-Reyna M, Hepp S, Pokorny R, Kroth PG, Essen LO, Kottke T
RgGuinier 3.4 nm
Dmax 12.6 nm
VolumePorod 115 nm3

SASDAV5 – apo XMRV RT

apo XMRV RT experimental SAS data
CRYSOL model
Sample: apo XMRV RT monomer, Escherichia coli protein
Buffer: 10 mM HEPES 100 mM KCl 5% Glycerol, pH: 6.5
Experiment: SAXS data collected at X33, DORIS III on 2011 Dec 8
Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid. Nucleic Acids Res 41(6):3874-87 (2013)
Nowak E, Potrzebowski W, Konarev PV, Rausch JW, Bona MK, Svergun DI, Bujnicki JM, Le Grice SF, Nowotny M
RgGuinier 4.0 nm
Dmax 13.5 nm
VolumePorod 160 nm3

SASDAW5 – XMRV RT + DNA/RNA hybrid

apo XMRV RTRNA_DNA hybrid substrate experimental SAS data
CRYSOL model
Sample: apo XMRV RT monomer, Escherichia coli protein
RNA_DNA hybrid substrate monomer, other
Buffer: 10 mM HEPES 100 mM KCl 5% Glycerol, pH: 6.5
Experiment: SAXS data collected at X33, DORIS III on 2011 Dec 8
Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid. Nucleic Acids Res 41(6):3874-87 (2013)
Nowak E, Potrzebowski W, Konarev PV, Rausch JW, Bona MK, Svergun DI, Bujnicki JM, Le Grice SF, Nowotny M
RgGuinier 3.5 nm
Dmax 11.5 nm
VolumePorod 155 nm3

SASDAN8 – mLBS1-2 DNA

MHV-68 TR DNA experimental SAS data
CRYSOL model
Sample: MHV-68 TR DNA monomer, unidentified herpesvirus DNA
Buffer: 10 mM TRIS 150 mM NaCl, pH: 7.6
Experiment: SAXS data collected at P12, PETRA III on 2013 Apr 27
KSHV but not MHV-68 LANA induces a strong bend upon binding to terminal repeat viral DNA. Nucleic Acids Res 43(20):10039-54 (2015)
...res de Miranda M, Carrondo MA, Simas JP, Kaye KM, Svergun DI, McVey CE
RgGuinier 4.0 nm
Dmax 16.0 nm
VolumePorod 50 nm3