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28 hits found for Petoukhov

SASDAP4 – Chitinase 60 from Moritella marina

Chitinase 60 experimental SAS data
Chitinase 60 from Moritella marina Rg histogram
Sample: Chitinase 60 monomer, 61 kDa Moritella marina protein
Buffer: 20 mM Tris 200 mM NaCl, pH: 8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Mar 18
Crystal structures of substrate-bound chitinase from the psychrophilic bacterium Moritella marina and its structure in solution. Acta Crystallogr D Biol Crystallogr 70(Pt 3):676-84 (2014)
...Petoukhov MV, Svergun DI, Rypniewski W
RgGuinier 3.2 nm
Dmax 11.3 nm
VolumePorod 75 nm3

SASDAQ8 – kLANA mutant dimer-tetramer mixture

ORF73 tetramerORF73 dimer experimental SAS data
NONE model
Sample: ORF73 tetramer tetramer, 63 kDa Human herpesvirus 8 protein
ORF73 dimer dimer, 32 kDa 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)
...Petoukhov MV, Correia B, Custodio TF, Juillard F, Tan M, Pires de Miranda M, Carrondo MA, Simas JP, Kaye KM, Svergun DI, McVey CE
RgGuinier 2.4 nm
Dmax 9.5 nm
VolumePorod 50 nm3

SASDAR4 – PTB full

Polypyrimidine tract-binding protein 1 experimental SAS data
BUNCH model
Sample: Polypyrimidine tract-binding protein 1 monomer, 57 kDa Homo sapiens protein
Buffer: 25 mM Tris 100 mM NaCl 5.0 mM DTT, pH: 7.2
Experiment: SAXS data collected at EMBL X33, DORIS III on 2004 Feb 11
Conformation of polypyrimidine tract binding protein in solution. Structure 14(6):1021-7 (2006)
Petoukhov MV, Monie TP, Allain FH, Matthews S, Curry S, Svergun DI
RgGuinier 4.0 nm
Dmax 16.5 nm

SASDAX2 – Pyruvate decarboxylase (PDC) from Z. mobilis

Pyruvate decarboxylase experimental SAS data
CRYSOL model
Sample: Pyruvate decarboxylase tetramer, 244 kDa Zymomonas mobilis protein
Buffer: 100 mM Sodium Citrate, 17% Glycerol, 22.5% PEG 1500, pH: 6
Experiment: SAXS data collected at EMBL X33, DORIS III on 1998 Nov 3
Crystal versus solution structures of thiamine diphosphate-dependent enzymes. J Biol Chem 275(1):297-302 (2000)
...Petoukhov MV, Koch MH, König S
RgGuinier 3.9 nm
Dmax 11.0 nm

SASDBC3 – RepB, the replication initiator protein of a promiscuous Streptococcal plasmid pMV158

Replication initiator protein of a promiscuous streptococcal plasmid pMV158. experimental SAS data
NONE model
Sample: Replication initiator protein of a promiscuous streptococcal plasmid pMV158. hexamer, Streptococcus sp. protein
Buffer: 10 mM TRIS 5 mM EDTA 1.0 M KCl, pH: 8.5
Experiment: SAXS data collected at EMBL X33, DORIS III on 2007 Jun 16
Conformational plasticity of RepB, the replication initiator protein of promiscuous streptococcal plasmid pMV158. Sci Rep 6:20915 (2016)
...Petoukhov MV, Machón C, Svergun DI, Orozco M, del Solar G, Coll M
RgGuinier 3.8 nm
Dmax 10.6 nm
VolumePorod 282 nm3

SASDAN3 – MutS dimer

DNA mismatch repair protein MutS experimental SAS data
DAMMIF model
Sample: DNA mismatch repair protein MutS dimer, 191 kDa Escherichia coli protein
Buffer: 50 mM HEPES 50 mM KCl, pH: 7.5
Experiment: SAXS data collected at EMBL 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)
...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, 381 kDa Escherichia coli protein
Buffer: 50 mM HEPES 50 mM KCl, pH: 7.5
Experiment: SAXS data collected at EMBL 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)
...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

SASDAV3 – Geminin:Cdt1 2:1 heterotrimer

GemininDNA replication factor Cdt1 experimental SAS data
CRYSOL model
Sample: Geminin dimer, 47 kDa Homo sapiens protein
DNA replication factor Cdt1 monomer, 60 kDa Homo sapiens protein
Buffer: 25 mM Tris75 200 mM NaCl, pH: 7.5
Experiment: SAXS data collected at EMBL X33, DORIS III on 2006 Aug 13
Quaternary structure of the human Cdt1-Geminin complex regulates DNA replication licensing. Proc Natl Acad Sci U S A 106(47):19807-12 (2009)
...Petoukhov MV, Iliou MS, Lygerou Z, Medema RH, Blow JJ, Svergun DI, Taraviras S, Perrakis A
RgGuinier 2.9 nm
Dmax 10.0 nm
VolumePorod 70 nm3

SASDAW3 – Geminin:Cdt1 4:2 heterohexamer

GemininDNA replication factor Cdt1 experimental SAS data
CRYSOL model
Sample: Geminin dimer, 47 kDa Homo sapiens protein
DNA replication factor Cdt1 monomer, 60 kDa Homo sapiens protein
Buffer: 25 mM Tris75 200 mM NaCl, pH: 7.5
Experiment: SAXS data collected at EMBL X33, DORIS III on 2006 Oct 5
Quaternary structure of the human Cdt1-Geminin complex regulates DNA replication licensing. Proc Natl Acad Sci U S A 106(47):19807-12 (2009)
...Petoukhov MV, Iliou MS, Lygerou Z, Medema RH, Blow JJ, Svergun DI, Taraviras S, Perrakis A
RgGuinier 3.8 nm
Dmax 14.0 nm
VolumePorod 120 nm3

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, 381 kDa Escherichia coli protein
Buffer: 50 mM HEPES 50 mM KCl, pH: 7.5
Experiment: SAXS data collected at EMBL 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)
...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

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, 381 kDa Escherichia coli protein
Buffer: 50 mM HEPES 50 mM KCl, pH: 7.5
Experiment: SAXS data collected at EMBL 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)
...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, 381 kDa Escherichia coli protein
Buffer: 50 mM HEPES 50 mM KCl, pH: 7.5
Experiment: SAXS data collected at EMBL 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)
...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, 381 kDa Escherichia coli protein
Buffer: 50 mM HEPES 50 mM KCl, pH: 7.5
Experiment: SAXS data collected at EMBL 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)
...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

SASDAH4 – DH-PH

DH-PH module of PDZRhoGEF experimental SAS data
DAMMIN model
Sample: DH-PH module of PDZRhoGEF monomer, 41 kDa Homo sapiens protein
Buffer: 50 mM Tris-HCL 150 mM NaCl 1.0 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL X33, DORIS III on 2008 Oct 30
The solution structure and dynamics of the DH-PH module of PDZRhoGEF in isolation and in complex with nucleotide-free RhoA. Protein Sci 18(10):2067-79 (2009)
...Petoukhov M, Zhang A, Fernandez EJ, Svergun DI, Derewenda U, Bushweller JH, Derewenda ZS
RgGuinier 2.9 nm
Dmax 9.0 nm
VolumePorod 60 nm3

SASDAM8 – MHV-68 LANA

Latency-associated nuclear antigen experimental SAS data
MHV-68 LANA Rg histogram
Sample: Latency-associated nuclear antigen tetramer, 87 kDa Murid herpesvirus 4 protein
Buffer: 25 mM Na/K Phosphate, pH: 7.5
Experiment: SAXS data collected at EMBL 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)
...Petoukhov MV, Correia B, Custodio TF, Juillard F, Tan M, Pires de Miranda M, Carrondo MA, Simas JP, Kaye KM, Svergun DI, McVey CE
RgGuinier 4.2 nm
Dmax 16.0 nm
VolumePorod 117 nm3

SASDAN8 – mLBS1-2 DNA

MHV-68 TR DNA experimental SAS data
CRYSOL model
Sample: MHV-68 TR DNA monomer, 30 kDa unidentified herpesvirus DNA
Buffer: 10 mM TRIS 150 mM NaCl, pH: 7.6
Experiment: SAXS data collected at EMBL 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)
...Petoukhov MV, Correia B, Custodio TF, Juillard F, Tan M, Pires de Miranda M, Carrondo MA, Simas JP, Kaye KM, Svergun DI, McVey CE
RgGuinier 4.0 nm
Dmax 16.0 nm
VolumePorod 50 nm3

SASDAP8 – kLBS1-2 DNA

kLBS1-2 DNA experimental SAS data
CRYSOL model
Sample: kLBS1-2 DNA monomer, 24 kDa 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)
...Petoukhov MV, Correia B, Custodio TF, Juillard F, Tan M, Pires de Miranda M, Carrondo MA, Simas JP, Kaye KM, Svergun DI, McVey CE
RgGuinier 4.0 nm
Dmax 16.0 nm
VolumePorod 50 nm3

SASDAQ4 – 6:3 complex of GAD:CaM

CalmodulinGlutamate decarboxylase experimental SAS data
BUNCH model
Sample: Calmodulin monomer, 17 kDa Homo sapiens protein
Glutamate decarboxylase hexamer, 340 kDa Petunia x hybrida protein
Buffer: 50 mM HEPES 50 mM KCl, pH: 7.5
Experiment: SAXS data collected at EMBL X33, DORIS III on 2004 Nov 9
A common structural basis for pH- and calmodulin-mediated regulation in plant glutamate decarboxylase. J Mol Biol 392(2):334-51 (2009)
...Petoukhov MV, Svergun DI, Grütter MG, Capitani G
RgGuinier 5.9 nm
Dmax 23.0 nm
VolumePorod 630 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, 30 kDa unidentified herpesvirus DNA
Latency-associated nuclear antigen octamer, 269 kDa Murid herpesvirus 4 protein
Buffer: 25 mM Na/K Phosphate, pH: 7.5
Experiment: SAXS data collected at EMBL 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)
...Petoukhov MV, Correia B, Custodio TF, Juillard F, Tan M, Pires de Miranda M, Carrondo MA, Simas JP, Kaye KM, Svergun DI, McVey CE
RgGuinier 5.8 nm
Dmax 20.0 nm
VolumePorod 475 nm3

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, 24 kDa unidentified herpesvirus DNA
ORF73 tetramer tetramer, 63 kDa Human herpesvirus 8 protein
ORF73 octamer octamer, 126 kDa Human herpesvirus 8 protein
kLBS1-2 DNA two monomers dimer, 48 kDa unidentified herpesvirus RNA
Buffer: 25 mM Na/K Phosphate, pH: 7.5
Experiment: SAXS data collected at EMBL 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)
...Petoukhov MV, Correia B, Custodio TF, Juillard F, Tan M, Pires de Miranda M, Carrondo MA, Simas JP, Kaye KM, Svergun DI, McVey CE
RgGuinier 4.8 nm
Dmax 16.0 nm
VolumePorod 250 nm3

SASDB45 – Trimeric periplasmic holdase chaperone protein Skp

Periplasmic holdase chaperone protein Skp experimental SAS data
Trimeric periplasmic holdase chaperone protein Skp Rg histogram
Sample: Periplasmic holdase chaperone protein Skp trimer, 47 kDa Escherichia coli protein
Buffer: 25 mM HEPES 150 mM NaCl 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Sep 24
A Spring-Loaded Mechanism Governs the Clamp-like Dynamics of the Skp Chaperone. Structure 25(7):1079-1088.e3 (2017)
...Petoukhov MV, Svergun DI, Hiller S, Bond PJ
RgGuinier 3.6 nm
Dmax 12.8 nm
VolumePorod 168 nm3

SASDAN4 – Calmodulin:peptide complex

CalmodulinC-terminal region of human myelin basic protein experimental SAS data
SASREF model
Sample: Calmodulin monomer, 17 kDa Homo sapiens protein
C-terminal region of human myelin basic protein monomer, 2 kDa Homo sapiens protein
Buffer: 25 mM Tris75 200 mM NaCl, pH: 7.5
Experiment: SAXS data collected at EMBL X33, DORIS III on 2006 Nov 28
Interaction between the C-terminal region of human myelin basic protein and calmodulin: analysis of complex formation and solution structure. BMC Struct Biol 8:10 (2008)
...Petoukhov MV, Hayashi N, Pirilä P, Svergun DI, Kursula P
RgGuinier 2.1 nm
Dmax 7.0 nm
VolumePorod 36 nm3

SASDDR9 – NADPH oxidase (H2O2 producing and [F-actin] oxidizing) MICAL1 (monomer)

[F-actin]-monooxygenase MICAL1 (monomer) experimental SAS data
CORAL model
Sample: [F-actin]-monooxygenase MICAL1 (monomer) monomer, 118 kDa Homo sapiens protein
Buffer: 50 mM sodium phosphate buffer, pH 7.5, 5 % glycerol, 100 mM NaCl, 1 mM EDTA, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2017 Jun 20
Human MICAL1: activation by the small GTPase Rab8 and small-angle X-ray scattering studies on the oligomerization state of MICAL1 and its complex with Rab8. Protein Sci (2018)
...Petoukhov MV, Rai A, Svergun DI, Vanoni MA
RgGuinier 3.7 nm
Dmax 12.1 nm
VolumePorod 212 nm3

SASDDS9 – NADPH oxidase (H2O2 producing and [F-actin] oxidizing) MICAL1 (monomer) (Truncated MOCHLIM construct)

[F-actin]-monooxygenase MICAL1 (MoChLim) experimental SAS data
CORAL model
Sample: [F-actin]-monooxygenase MICAL1 (MoChLim) monomer, 85 kDa Homo sapiens protein
Buffer: 20 mM Hepes/NaOH, pH 7.5, 50 mM NaCl, 2 mM MgCl2, 2 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2017 Jun 20
Human MICAL1: activation by the small GTPase Rab8 and small-angle X-ray scattering studies on the oligomerization state of MICAL1 and its complex with Rab8. Protein Sci (2018)
...Petoukhov MV, Rai A, Svergun DI, Vanoni MA
RgGuinier 4.0 nm
Dmax 18.0 nm
VolumePorod 145 nm3

SASDDT9 – NADPH oxidase (H2O2 producing and [F-actin] oxidizing) MICAL1 (monomer) in complex with Ras-related protein Rab 8 (MICAL1-Rab8 complex)

[F-actin]-monooxygenase MICAL1 (monomer)Ras-related protein 8 experimental SAS data
CORAL model
Sample: [F-actin]-monooxygenase MICAL1 (monomer) monomer, 118 kDa Homo sapiens protein
Ras-related protein 8 monomer, 20 kDa protein
Buffer: 20 mM Hepes/NaOH, pH 7.5, 50 mM NaCl, 2 mM MgCl2, 2 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2017 Jun 20
Human MICAL1: activation by the small GTPase Rab8 and small-angle X-ray scattering studies on the oligomerization state of MICAL1 and its complex with Rab8. Protein Sci (2018)
...Petoukhov MV, Rai A, Svergun DI, Vanoni MA
RgGuinier 3.7 nm
Dmax 11.8 nm
VolumePorod 234 nm3

SASDDU9 – NADPH oxidase (H2O2 producing and [F-actin] oxidizing) MICAL1 (monomer) (Truncated MOCH construct)

[F-actin]-monooxygenase MICAL1 (MoCh) experimental SAS data
PDB model
Sample: [F-actin]-monooxygenase MICAL1 (MoCh) monomer, 67 kDa Homo sapiens protein
Buffer: 50 mM sodium phosphate buffer, 5 % glycerol, 100 mM NaCl, 1 mM EDTA, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2016 Jun 6
Human MICAL1: activation by the small GTPase Rab8 and small-angle X-ray scattering studies on the oligomerization state of MICAL1 and its complex with Rab8. Protein Sci (2018)
...Petoukhov MV, Rai A, Svergun DI, Vanoni MA
RgGuinier 3.4 nm
Dmax 12.0 nm
VolumePorod 100 nm3

SASDAX5 – Endophilin-CoA complex

Endophilin-A1 BAR domainarachidonyl-CoA experimental SAS data
SASREF model
Sample: Endophilin-A1 BAR domain dimer, 58 kDa Mus musculus protein
arachidonyl-CoA , 60 kDa
Buffer: 50 mM TRIS-HCL 300 mM NaCl, pH: 8
Experiment: SAXS data collected at EMBL X33, DORIS III on 2006 Nov 27
Endophilin-A1 BAR domain interaction with arachidonyl CoA. Front Mol Biosci 1:20 (2014)
Petoukhov MV, Weissenhorn W, Svergun DI
RgGuinier 5.9 nm
Dmax 19.0 nm
VolumePorod 480 nm3

SASDAY5 – Free endophilin

Endophilin-A1 BAR domain experimental SAS data
CORAL model
Sample: Endophilin-A1 BAR domain dimer, 58 kDa Mus musculus protein
Buffer: 50 mM TRIS-HCL 300 mM NaCl, pH: 8
Experiment: SAXS data collected at EMBL X33, DORIS III on 2004 Feb 13
Endophilin-A1 BAR domain interaction with arachidonyl CoA. Front Mol Biosci 1:20 (2014)
Petoukhov MV, Weissenhorn W, Svergun DI
RgGuinier 3.3 nm
Dmax 13.5 nm
VolumePorod 90 nm3