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12 hits found for Histone H2B

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

SASDBY4 – ...histone H2A/H2B complex

Nucleoplasmin core + A2Histone H2A (ΔAla127)Histone H2B 1.1 (Ser33Thr) experimental SAS data
DAMFILT model
Sample: Nucleoplasmin core + A2 pentamer, 81 kDa Xenopus laevis protein
Histone H2A (ΔAla127) pentamer, 69 kDa Xenopus laevis protein
Histone H2B 1.1 (Ser33Thr) pentamer, 67 kDa Xenopus laevis protein
Buffer: 20 mM Tris. 150 mM NaCl, 1 mM EDTA, 5 mM DTT, pH: 8
Experiment: SAXS data collected at BL4-2, Stanford Synchrotron Radiation Lightsource (SSRL) on 2016 Jan 7
...histone chaperone nucleoplasmin controls histone binding and release. Nat Commun 8(1):2215 (2017)
Warren C, Matsui T, Karp JM, Onikubo T, Cahill S, Brenowitz M, Cowburn D, Girvin M, Shechter D
RgGuinier 4.4 nm
Dmax 14.0 nm
VolumePorod 402 nm3

SASDJJ5 – Histone H2A:H2B:H3:H4 complex with aprataxin and polynucleotide kinase like factor (APLF) acidic domain

Aprataxin and PNK-like factor (acidic domain)Histone H2AHistone H2BHistone H3Histone H4 experimental SAS data
DAMMIF model
Sample: Aprataxin and PNK-like factor (acidic domain) dimer, 15 kDa Homo sapiens protein
Histone H2A dimer, 26 kDa Drosophila melanogaster protein
Histone H2B dimer, 27 kDa Drosophila melanogaster protein
Histone H3 dimer, 30 kDa Drosophila melanogaster protein
Histone H4 dimer, 23 kDa Drosophila melanogaster protein
Buffer: 25 mM NaPi, 300 mM NaCl, 3% v/v glycerol, 1 mM DTT,, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Jul 10
...histone octamer by the acidic domain of DNA repair factor APLF. Sci Adv 8(30):eabo0517 (2022)
Corbeski I, Guo X, Eckhardt BV, Fasci D, Wiegant W, Graewert MA, Vreeken K, Wienk H, Svergun DI, Heck AJR, van Attikum H, Boelens R, Sixma TK, Mattiroli F, van Ingen H
RgGuinier 3.7 nm
Dmax 10.8 nm
VolumePorod 260 nm3

SASDJ96 – Trinucleosomes from Xenopus laevis (African clawed frog)

Histone H3Histone H4Histone H2A type 1Histone H2BNon-linker Ended Trinucleosome DNA experimental SAS data
Histone H3 Histone H4 Histone H2A type 1 Histone H2B Non-linker Ended Trinucleosome DNA Kratky plot
Sample: Histone H3 monomer, 15 kDa Xenopus laevis protein
Histone H4 monomer, 11 kDa Xenopus laevis protein
Histone H2A type 1 monomer, 14 kDa Xenopus laevis protein
Histone H2B monomer, 14 kDa Xenopus laevis protein
Non-linker Ended Trinucleosome DNA monomer, 172 kDa DNA
Buffer: 20 mM Tris 150 mM NaCl 1 mM EDTA 1 mM DTT 50% w/v sucrose, pH: 7.5
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2016 Mar 11
Solution structure(s) of trinucleosomes from contrast variation SAXS Nucleic Acids Research (2021)
Mauney A, Muthurajan U, Luger K, Pollack L
RgGuinier 12.9 nm
Dmax 41.8 nm

SASDCT6 – 12N12 nucleosome in 60% sucrose with ADP-BeF3

169 bp DNA (145 bp Widom 601, flanked by 12bp DNA)Histone H2A type 1Histone H2B 1.1Histone H3.2Histone H4 experimental SAS data
12N12 nucleosome in 60% sucrose with ADP-BeF3 Rg histogram
Sample: 169 bp DNA (145 bp Widom 601, flanked by 12bp DNA) monomer, 52 kDa DNA
Histone H2A type 1 monomer, 14 kDa Xenopus laevis protein
Histone H2B 1.1 monomer, 14 kDa Xenopus laevis protein
Histone H3.2 monomer, 15 kDa Xenopus laevis protein
Histone H4 monomer, 11 kDa Xenopus laevis protein
Buffer: 10 mM Tris, 100 mM NaCl, 2 mM MgCl2, 0.1 mM EDTA, 1 mM DTT, 60% (w/v) sucrose, ADP-BeF3 (0.5 mM ADP, 4 mM NaF, 0.6 mM BeCl2), pH: 7.8
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2015 Oct 24
The ATPase motor of the Chd1 chromatin remodeler stimulates DNA unwrapping from the nucleosome. Nucleic Acids Res 46(10):4978-4990 (2018)
Tokuda JM, Ren R, Levendosky RF, Tay RJ, Yan M, Pollack L, Bowman GD
RgGuinier 4.8 nm
Dmax 14.0 nm

SASDCU6 – Chd1-12N12, chromatin remodeler--nucleosome complex, in 60% sucrose without any nucleotides added (Apo)

Chromodomain-helicase-DNA-binding protein 1169 bp DNA (145 bp Widom 601, flanked by 12bp DNA)Histone H2A type 1Histone H2B 1.1Histone H3.2Histone H4 experimental SAS data
Chd1-12N12, chromatin remodeler--nucleosome complex, in 60% sucrose without any nucleotides added (Apo) Rg histogram
Sample: Chromodomain-helicase-DNA-binding protein 1 dimer, 266 kDa Saccharomyces cerevisiae protein
169 bp DNA (145 bp Widom 601, flanked by 12bp DNA) monomer, 52 kDa DNA
Histone H2A type 1 monomer, 14 kDa Xenopus laevis protein
Histone H2B 1.1 monomer, 14 kDa Xenopus laevis protein
Histone H3.2 monomer, 15 kDa Xenopus laevis protein
Histone H4 monomer, 11 kDa Xenopus laevis protein
Buffer: 10 mM Tris, 100 mM NaCl, 2 mM MgCl2, 0.1 mM EDTA, 1 mM DTT, 60% (w/v) sucrose, pH: 7.8
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2015 Oct 24
The ATPase motor of the Chd1 chromatin remodeler stimulates DNA unwrapping from the nucleosome. Nucleic Acids Res 46(10):4978-4990 (2018)
Tokuda JM, Ren R, Levendosky RF, Tay RJ, Yan M, Pollack L, Bowman GD
RgGuinier 5.2 nm
Dmax 12.8 nm

SASDCV6 – Chd1-12N12, chromatin remodeler--nucleosome complex, in 60% sucrose with ADP-BeF3

Chromodomain-helicase-DNA-binding protein 1169 bp DNA (145 bp Widom 601, flanked by 12bp DNA)Histone H2A type 1Histone H2B 1.1Histone H3.2Histone H4 experimental SAS data
Chd1-12N12, chromatin remodeler--nucleosome complex, in 60% sucrose with ADP-BeF3 Rg histogram
Sample: Chromodomain-helicase-DNA-binding protein 1 dimer, 266 kDa Saccharomyces cerevisiae protein
169 bp DNA (145 bp Widom 601, flanked by 12bp DNA) monomer, 52 kDa DNA
Histone H2A type 1 monomer, 14 kDa Xenopus laevis protein
Histone H2B 1.1 monomer, 14 kDa Xenopus laevis protein
Histone H3.2 monomer, 15 kDa Xenopus laevis protein
Histone H4 monomer, 11 kDa Xenopus laevis protein
Buffer: 10 mM Tris, 100 mM NaCl, 2 mM MgCl2, 0.1 mM EDTA, 1 mM DTT, 60% (w/v) sucrose, ADP-BeF3 (0.5 mM ADP, 4 mM NaF, 0.6 mM BeCl2), pH: 7.8
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2015 Oct 24
The ATPase motor of the Chd1 chromatin remodeler stimulates DNA unwrapping from the nucleosome. Nucleic Acids Res 46(10):4978-4990 (2018)
Tokuda JM, Ren R, Levendosky RF, Tay RJ, Yan M, Pollack L, Bowman GD
RgGuinier 5.3 nm
Dmax 16.5 nm

SASDCW6 – Chd1-12N12, chromatin remodeler--nucleosome complex, in 60% sucrose with AMP-PNP

Chromodomain-helicase-DNA-binding protein 1169 bp DNA (145 bp Widom 601, flanked by 12bp DNA)Histone H2A type 1Histone H2B 1.1Histone H3.2Histone H4 experimental SAS data
Chd1-12N12, chromatin remodeler--nucleosome complex, in 60% sucrose with AMP-PNP Rg histogram
Sample: Chromodomain-helicase-DNA-binding protein 1 dimer, 266 kDa Saccharomyces cerevisiae protein
169 bp DNA (145 bp Widom 601, flanked by 12bp DNA) monomer, 52 kDa DNA
Histone H2A type 1 monomer, 14 kDa Xenopus laevis protein
Histone H2B 1.1 monomer, 14 kDa Xenopus laevis protein
Histone H3.2 monomer, 15 kDa Xenopus laevis protein
Histone H4 monomer, 11 kDa Xenopus laevis protein
Buffer: 10 mM Tris, 100 mM NaCl, 2 mM MgCl2, 0.1 mM EDTA, 1 mM DTT, 60% (w/v) sucrose, 0.5 mM AMP-PNP, pH: 7.8
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2015 Oct 24
The ATPase motor of the Chd1 chromatin remodeler stimulates DNA unwrapping from the nucleosome. Nucleic Acids Res 46(10):4978-4990 (2018)
Tokuda JM, Ren R, Levendosky RF, Tay RJ, Yan M, Pollack L, Bowman GD
RgGuinier 5.6 nm
Dmax 16.7 nm

SASDBS7 – Nucleosome Core Particle: 1.2 M NaCl, 50% sucrose, 50ms - 10s time resolved data

Nucleasome Core Particle with Widom 601 DNA - HISTONE H2A-H2B HeterodimerNucleasome Core Particle with Widom 601 DNA - HISTONE H3-H4 HeterodimerNucleasome Core Particle with Widom 601 DNA - dsDNA experimental SAS data
Nucleasome Core Particle with Widom 601 DNA - HISTONE H2A-H2B Heterodimer Nucleasome Core Particle with Widom 601 DNA - HISTONE H3-H4 Heterodimer Nucleasome Core Particle with Widom 601 DNA - dsDNA Kratky plot
Sample: ...HISTONE H2A-H2B Heterodimer dimer, 48 kDa Xenopus laevis protein
...HISTONE H3-H4 Heterodimer dimer, 46 kDa Xenopus laevis protein
Nucleasome Core Particle with Widom 601 DNA - dsDNA monomer, 92 kDa Xenopus laevis DNA
Buffer: 20 mM Tris-Cl, 0.1 mM EDTA, 0.1 mM DTT, 50% sucrose, 1.2 M NaCl, pH: 7.5
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2014 Apr 14
...histone core. Proc Natl Acad Sci U S A 114(2):334-339 (2017)
Chen Y, Tokuda JM, Topping T, Meisburger SP, Pabit SA, Gloss LM, Pollack L
RgGuinier 5.8 nm

SASDBT7 – Nucleosome Core Particle: 1.9 M NaCl, 50% sucrose, 50ms - 10s time resolved data

Nucleasome Core Particle with Widom 601 DNA - HISTONE H2A-H2B HeterodimerNucleasome Core Particle with Widom 601 DNA - HISTONE H3-H4 HeterodimerNucleasome Core Particle with Widom 601 DNA - dsDNA experimental SAS data
Nucleasome Core Particle with Widom 601 DNA - HISTONE H2A-H2B Heterodimer Nucleasome Core Particle with Widom 601 DNA - HISTONE H3-H4 Heterodimer Nucleasome Core Particle with Widom 601 DNA - dsDNA Kratky plot
Sample: ...HISTONE H2A-H2B Heterodimer dimer, 48 kDa Xenopus laevis protein
...HISTONE H3-H4 Heterodimer dimer, 46 kDa Xenopus laevis protein
Nucleasome Core Particle with Widom 601 DNA - dsDNA monomer, 92 kDa Xenopus laevis DNA
Buffer: 20 mM Tris-Cl, 0.1 mM EDTA, 0.1 mM DTT, 50% sucrose, 1.9 M NaCl, pH: 7.5
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2014 Apr 14
...histone core. Proc Natl Acad Sci U S A 114(2):334-339 (2017)
Chen Y, Tokuda JM, Topping T, Meisburger SP, Pabit SA, Gloss LM, Pollack L
RgGuinier 6.8 nm

SASDNR7 – ...H2B histone oligomer complex

Peptidyl-prolyl cis-trans isomerase FKBP43Histone H2A type 1-B/EHistone H2B type 1-C/E/F/G/I experimental SAS data
MULTIFOXS model
Sample: Peptidyl-prolyl cis-trans isomerase FKBP43 pentamer, 81 kDa Arabidopsis thaliana protein
Histone H2A type 1-B/E monomer, 14 kDa Homo sapiens protein
Histone H2B type 1-C/E/F/G/I monomer, 14 kDa Homo sapiens protein
Buffer: 20 mM Tris, 300 mM NaCl, 1 mM β-mercaptoethanol, pH: 7.5
Experiment: SAXS data collected at BM29, ESRF on 2021 Apr 28
...histone interaction. Biochim Biophys Acta Gene Regul Mech 1865(7):194872 (2022)
Singh AK, Saharan K, Baral S, Vasudevan D
RgGuinier 4.1 nm
Dmax 13.9 nm
VolumePorod 194 nm3