MACROMOLECULE TYPE: heterocomplex

SASDHL3 – Braveheart Fragment 1 + Cellular nucleic acid-binding protein (CNBP)

Cellular nucleic acid-binding proteinBraveheart Fragment 1 experimental SAS data
DAMMIN model
Sample: Cellular nucleic acid-binding protein monomer, 22 kDa Homo sapiens protein
Braveheart Fragment 1 monomer, 116 kDa Homo sapiens RNA
Buffer: 50 mM HEPES-KOH, 100 mM KCl, 6 mM MgCl2, pH: 7.6
Experiment: SAXS data collected at B21, Diamond Light Source on 2018 Jun 23
Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution Nature Communications 11(1) (2020)
Kim D, Thiel B, Mrozowich T, Hennelly S, Hofacker I, Patel T, Sanbonmatsu K
RgGuinier 8.2 nm
Dmax 27.0 nm
VolumePorod 455 nm3

SASDF29 – Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 4 - in complex with STAU1 binding site within the ADP-ribosylation factor1

Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 4ADP-ribosylation factor1 - short experimental SAS data
OTHER model
Sample: Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 4 monomer, 8 kDa Homo sapiens protein
ADP-ribosylation factor1 - short monomer, 11 kDa Homo sapiens RNA
Buffer: 50 mM potassium phosphate, 100 mM NaCl, 3.5 mM 2-mercaptoethanol, pH: 6.8
Experiment: SAXS data collected at Rigaku BioSAXS-1000, CEITEC on 2015 Dec 10
Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition. Nucleic Acids Res (2019)
Yadav DK, Zigáčková D, Zlobina M, Klumpler T, Beaumont C, Kubíčková M, Vaňáčová Š, Lukavsky PJ
RgGuinier 1.7 nm
Dmax 6.0 nm
VolumePorod 21 nm3

SASDF39 – Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4 - in complex with STAU1 binding site within the ADP-ribosylation factor1

ADP-ribosylation factor1 - shortDouble-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4 experimental SAS data
OTHER model
Sample: ADP-ribosylation factor1 - short monomer, 11 kDa Homo sapiens RNA
Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4 monomer, 20 kDa Homo sapiens protein
Buffer: 50 mM sodium phosphate buffer, 300 mM NaCl, 500 mM imidazole, pH: 8
Experiment: SAXS data collected at Rigaku BioSAXS-1000, CEITEC on 2018 May 29
Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition. Nucleic Acids Res (2019)
Yadav DK, Zigáčková D, Zlobina M, Klumpler T, Beaumont C, Kubíčková M, Vaňáčová Š, Lukavsky PJ
RgGuinier 2.1 nm
Dmax 6.4 nm
VolumePorod 39 nm3

SASDF49 – Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4 - in complex with STAU1 binding site within the ADP-ribosylation factor1 - long

Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4ADP-ribosylation factor1 - long experimental SAS data
Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4 ADP-ribosylation factor1 - long Kratky plot
Sample: Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4 monomer, 20 kDa Homo sapiens protein
ADP-ribosylation factor1 - long monomer, 16 kDa Homo sapiens RNA
Buffer: 50 mM potassium phosphate, 100 mM NaCl, 3.5 mM 2-mercaptoethanol, pH: 6.8
Experiment: SAXS data collected at B21, Diamond Light Source on 2018 Sep 20
Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition. Nucleic Acids Res (2019)
Yadav DK, Zigáčková D, Zlobina M, Klumpler T, Beaumont C, Kubíčková M, Vaňáčová Š, Lukavsky PJ
RgGuinier 2.5 nm
Dmax 7.0 nm
VolumePorod 53 nm3

SASDDG3 – Solution Structure of Archaeal Biofilm Regulator 2 (AbfR2) in Complex with DNA

Sa0446 binding sequence 40bpTranscriptional regulator Lrs14-like protein experimental SAS data
DAMMIF model
Sample: Sa0446 binding sequence 40bp monomer, 25 kDa DNA
Transcriptional regulator Lrs14-like protein dimer, 33 kDa Sulfolobus acidocaldarius protein
Buffer: 300 mM NaCl, 20 mM HEPES, pH 7.5, pH: 7.5
Experiment: SAXS data collected at BM29, ESRF on 2016 Nov 5
Solution Structure of Archaeal Biofilm Regulator 2 (AbfR2) in Complex with 40 bp DNA
Marian Vogt
RgGuinier 3.4 nm
Dmax 12.8 nm
VolumePorod 60 nm3

SASDGT2 – Thymine dioxygenase J-containing DNA binding domain in complex with J-23-DNA (JDBD:J-23-DNA)

J-DNA binding domainJ-DNA (23mer) experimental SAS data
J-DNA binding domain J-DNA (23mer) Kratky plot
Sample: J-DNA binding domain monomer, 21 kDa Leishmania tarentolae protein
J-DNA (23mer) monomer, 14 kDa DNA
Buffer: 20 mM HEPES, 200 mM NaCl, 1 mM TCEP, pH: 7.5
Experiment: SAXS data collected at BM29, ESRF on 2016 Feb 21
The domain architecture of protozoan protein J-DNA-binding protein 1 suggests synergy between base J DNA binding and thymidine hydroxylase activity. J Biol Chem (2019)
Adamopoulos A, Heidebrecht T, Roosendaal J, Touw WG, Phan IQ, Beijnen J, Perrakis A
RgGuinier 2.5 nm
Dmax 8.6 nm
VolumePorod 43 nm3

SASDGU2 – Thymine dioxygenase full length J-DNA binding protein in complex with J-23-DNA (JBP1:J-23-DNA)

Thymine dioxygenase JBP1J-DNA (23mer) experimental SAS data
Thymine dioxygenase JBP1 J-DNA (23mer) Kratky plot
Sample: Thymine dioxygenase JBP1 monomer, 93 kDa Leishmania tarentolae protein
J-DNA (23mer) monomer, 14 kDa DNA
Buffer: 20 mM HEPES, 200 mM NaCl, 1 mM TCEP, pH: 7.5
Experiment: SAXS data collected at BM29, ESRF on 2016 Feb 21
The domain architecture of protozoan protein J-DNA-binding protein 1 suggests synergy between base J DNA binding and thymidine hydroxylase activity. J Biol Chem (2019)
Adamopoulos A, Heidebrecht T, Roosendaal J, Touw WG, Phan IQ, Beijnen J, Perrakis A
RgGuinier 4.1 nm
Dmax 14.1 nm
VolumePorod 148 nm3

SASDF62 – Mixture of the dsRBD1 and dsRBD2 domains of Drosophila helicase dosage compensation regulator, MLE, and the roX2 RNA stem-loop 7 18mer-fragment, at 1.0 mg/ml

Dosage compensation regulatorroX2 stem-loop 7, 18-mer fragment experimental SAS data
Dosage compensation regulator roX2 stem-loop 7, 18-mer fragment Kratky plot
Sample: Dosage compensation regulator monomer, 29 kDa Drosophila melanogaster protein
RoX2 stem-loop 7, 18-mer fragment monomer, 12 kDa synthetic construct RNA
Buffer: 20 mM NaPO4, 200 mM NaCl, 1 mM DTT, pH: 6.5
Experiment: SAXS data collected at BM29, ESRF on 2016 Nov 29
Structure, dynamics and roX2-lncRNA binding of tandem double-stranded RNA binding domains dsRBD1,2 of Drosophila helicase Maleless. Nucleic Acids Res 47(8):4319-4333 (2019)
Ankush Jagtap PK, Müller M, Masiewicz P, von Bülow S, Hollmann NM, Chen PC, Simon B, Thomae AW, Becker PB, Hennig J
RgGuinier 3.1 nm
Dmax 13.3 nm
VolumePorod 25 nm3

SASDFX3 – Semi-synthetic nucleosome core particle (NCP)

Histone H3Histone H4Histone H2aHistone H2b147bp 601 Widom sequence experimental SAS data
Histone H3 Histone H4 Histone H2a Histone H2b 147bp 601 Widom sequence Kratky plot
Sample: Histone H3 dimer, 31 kDa Xenopus laevis protein
Histone H4 dimer, 22 kDa Xenopus laevis protein
Histone H2a dimer, 28 kDa Xenopus laevis protein
Histone H2b dimer, 27 kDa Xenopus laevis protein
147bp 601 Widom sequence monomer, 45 kDa synthetic construct DNA
Buffer: 15 mM HEPES, 200 mM NaCl, pH: 7.3
Experiment: SAXS data collected at BM29, ESRF on 2017 Dec 11
A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex. Cell Rep 27(2):387-399.e7 (2019)
Marabelli C, Marrocco B, Pilotto S, Chittori S, Picaud S, Marchese S, Ciossani G, Forneris F, Filippakopoulos P, Schoehn G, Rhodes D, Subramaniam S, Mattevi A
RgGuinier 4.4 nm
Dmax 12.8 nm
VolumePorod 353 nm3

SASDFY3 – Semi-synthetic nucleosome core particle (NCP) in complex with lysine-specific demethylase (LSD2) and the dehydrogenase domain plus linker of cytokine-like nuclear factor (NPAC delta-205)

Lysyne-specific Demethylase LSD2NPAC linker+DH (delta-205)Histone H3Histone H4Histone H2aHistone H2b147bp 601 Widom sequence experimental SAS data
Lysyne-specific Demethylase LSD2 NPAC linker+DH (delta-205) Histone H3 Histone H4 Histone H2a Histone H2b 147bp 601 Widom sequence Kratky plot
Sample: Lysyne-specific Demethylase LSD2 monomer, 89 kDa Homo sapiens protein
NPAC linker+DH (delta-205) tetramer, 150 kDa Homo sapiens protein
Histone H3 dimer, 31 kDa Xenopus laevis protein
Histone H4 dimer, 22 kDa Xenopus laevis protein
Histone H2a dimer, 28 kDa Xenopus laevis protein
Histone H2b dimer, 27 kDa Xenopus laevis protein
147bp 601 Widom sequence monomer, 45 kDa synthetic construct DNA
Buffer: 15 mM HEPES, 200 mM NaCl, pH: 7.3
Experiment: SAXS data collected at BM29, ESRF on 2017 Dec 11
A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex. Cell Rep 27(2):387-399.e7 (2019)
Marabelli C, Marrocco B, Pilotto S, Chittori S, Picaud S, Marchese S, Ciossani G, Forneris F, Filippakopoulos P, Schoehn G, Rhodes D, Subramaniam S, Mattevi A
RgGuinier 7.8 nm
Dmax 30.4 nm
VolumePorod 1100 nm3