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8x7k

Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination)

Method: ELECTRON MICROSCOPY Dmax: 126.9 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone H3.2

Homo sapiens

UniProt Q71DI3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 10 DNA 2 PDB declaration: dodecameric（12） Consistent with all polymer counts Chain A； UniProt 39–135 Chain E； UniProt 39–135 Not recorded Histone H4 × 2 （P62805） Histone H2A type 1-B/E × 1 （P04908） Histone H2B type 1-K × 2 （O60814） Histone H2A type 1-B/E × 1 （P04908） DNA (143-MER) × 1 DNA (143-MER) × 1 Ubiquitin-conjugating enzyme E2 D3 × 1 （P61077） E3 ubiquitin-protein ligase RNF168 × 1 （Q8IYW5） ZN ZINC ION × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.27 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8X7K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
10XZ Non-damaged nucleosome Deposited 2026-02-12 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
10YA Nucleosome containing a nick at SHL-4 Deposited 2026-02-12 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
10YB Nucleosome containing a nick at SHL-2 Deposited 2026-02-12 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
10YC Nucleosome containing a nick at SHL-4 Deposited 2026-02-12 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
10YD Nucleosome containing a nick at SHL-6 Deposited 2026-02-12 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
10YE DNA Ligase IIIa bound to nucleosome containing a nick at SHL0 Deposited 2026-02-12 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain A 39–135（97 aa）
Chain E 39–135（97 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
10YF DNA Ligase IIIa bound to nucleosome containing a nick at SHL-2 (composite) Deposited 2026-02-12 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain A 39–134（96 aa）
Chain E 39–134（96 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution not provided
10YG DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-4 (composite) Deposited 2026-02-12 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain A 39–135（97 aa）
Chain E 39–135（97 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution not provided
10YH DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-6 (composite) Deposited 2026-02-12 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain A 39–135（97 aa）
Chain E 39–135（97 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
10YI XRCC1-DNA Ligase IIIa complex bound to a nucleosome containing a nick at SHL-6 (composite) Deposited 2026-02-12 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain A 39–135（97 aa）
Chain E 39–135（97 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
2X4W Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1. Deposited 2010-02-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 23–43（21 aa） Fragment：RESIDUES 23-43
Non-standard monomer：Yes (specific site not provided by mmCIF) FMT FORMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；4M SODIUM FORMATE, 0.1M TRIS (PH 8.5), 0.01M NACL
Resolution 1.50 Å R-free 0.216
2X4X Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1. Deposited 2010-02-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 23–43（21 aa） Fragment：RESIDUES 23-43
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；20% PEG3350, 0.2M LITHIUM SULPHATE, 0.1M TRIS (PH 8.5) 0.01M NACL
Resolution 1.85 Å R-free 0.239
2X4X Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1. Deposited 2010-02-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 23–43（21 aa） Fragment：RESIDUES 23-43
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；20% PEG3350, 0.2M LITHIUM SULPHATE, 0.1M TRIS (PH 8.5) 0.01M NACL
Resolution 1.85 Å R-free 0.239
2X4X Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1. Deposited 2010-02-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 23–43（21 aa） Fragment：RESIDUES 23-43
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；20% PEG3350, 0.2M LITHIUM SULPHATE, 0.1M TRIS (PH 8.5) 0.01M NACL
Resolution 1.85 Å R-free 0.239
2X4X Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1. Deposited 2010-02-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 23–43（21 aa） Fragment：RESIDUES 23-43
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；20% PEG3350, 0.2M LITHIUM SULPHATE, 0.1M TRIS (PH 8.5) 0.01M NACL
Resolution 1.85 Å R-free 0.239
2X4Y Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1. Deposited 2010-02-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 23–43（21 aa） Fragment：RESIDUES 23-43
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；30% PEG4K, 0.2M LITHIUM SULPHATE, 0.1M TRIS (PH 8.5), 0.01M NACL.
Resolution 1.70 Å R-free 0.227
2X4Y Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1. Deposited 2010-02-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 23–43（21 aa） Fragment：RESIDUES 23-43
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；30% PEG4K, 0.2M LITHIUM SULPHATE, 0.1M TRIS (PH 8.5), 0.01M NACL.
Resolution 1.70 Å R-free 0.227
2X4Y Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1. Deposited 2010-02-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 23–43（21 aa） Fragment：RESIDUES 23-43
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；30% PEG4K, 0.2M LITHIUM SULPHATE, 0.1M TRIS (PH 8.5), 0.01M NACL.
Resolution 1.70 Å R-free 0.227
2X4Y Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1. Deposited 2010-02-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 23–43（21 aa） Fragment：RESIDUES 23-43
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；30% PEG4K, 0.2M LITHIUM SULPHATE, 0.1M TRIS (PH 8.5), 0.01M NACL.
Resolution 1.70 Å R-free 0.227
2X4Y Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1. Deposited 2010-02-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 23–43（21 aa） Fragment：RESIDUES 23-43
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；30% PEG4K, 0.2M LITHIUM SULPHATE, 0.1M TRIS (PH 8.5), 0.01M NACL.
Resolution 1.70 Å R-free 0.227
2X4Y Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1. Deposited 2010-02-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain N 23–43（21 aa） Fragment：RESIDUES 23-43
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；30% PEG4K, 0.2M LITHIUM SULPHATE, 0.1M TRIS (PH 8.5), 0.01M NACL.
Resolution 1.70 Å R-free 0.227
2X4Y Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1. Deposited 2010-02-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain J 23–43（21 aa） Fragment：RESIDUES 23-43
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；30% PEG4K, 0.2M LITHIUM SULPHATE, 0.1M TRIS (PH 8.5), 0.01M NACL.
Resolution 1.70 Å R-free 0.227
2X4Y Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1. Deposited 2010-02-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 23–43（21 aa） Fragment：RESIDUES 23-43
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；30% PEG4K, 0.2M LITHIUM SULPHATE, 0.1M TRIS (PH 8.5), 0.01M NACL.
Resolution 1.70 Å R-free 0.227
3AV1 The human nucleosome structure containing the histone variant H3.2 Deposited 2011-02-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.290
3DB3 Crystal structure of the tandem tudor domains of the E3 ubiquitin-protein ligase UHRF1 in complex with trimethylated histone H3-K9 peptide Deposited 2008-05-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 7–12（6 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；3 M SODIUM FORMATE, 0.1 M SODIUM ACETATE, pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.282
3MO8 PWWP Domain of Human Bromodomain and PHD finger-containing protein 1 In Complex with Trimethylated H3K36 Peptide Deposited 2010-04-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 31–42（12 aa） Fragment：UNP residue 31-42
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；3.5M sodium formate, 0.1M Tris-HCl pH8.5, H3K36me3 peptide, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.69 Å R-free 0.207
4MZF Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2a) peptide Deposited 2013-09-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–10（9 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291.15 K；20% PEG 8000, 20% PEG 400, 0.1M MgCl2, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K
Resolution 2.10 Å R-free 0.255
4MZG Crystal structure of human Spindlin1 bound to histone H3K4me3 peptide Deposited 2013-09-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–21（20 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291.15 K；37.5% MPD_P1K_P3350, 0.1M bicine/Trizma, pH 8.5, 0.06M MgCl2/CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K
Resolution 1.70 Å R-free 0.207
4MZG Crystal structure of human Spindlin1 bound to histone H3K4me3 peptide Deposited 2013-09-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–21（20 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291.15 K；37.5% MPD_P1K_P3350, 0.1M bicine/Trizma, pH 8.5, 0.06M MgCl2/CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K
Resolution 1.70 Å R-free 0.207
4MZH Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2s) peptide Deposited 2013-09-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–10（9 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291.15 K；20% PEG 8000, 20% PEG 400, 0.1M MgCl2, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K
Resolution 2.20 Å R-free 0.247
4OUC Structure of human haspin in complex with histone H3 substrate Deposited 2014-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–13（12 aa） Fragment：histone H3 tail, UNP residues 2-13
Not recorded NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 6 5ID (2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL × 1 IOD IODIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277.15 K；20% PEG 3350, 0.2M potassium thiocyanate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Resolution 1.90 Å R-free 0.211
5B0Y Crystal structure of the nucleosome containing histone H3 with the crotonylated lysine 122 Deposited 2015-11-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.56 Å R-free 0.249
5B0Z The crystal structure of the nucleosome containing H3.2, at 1.98 A resolution Deposited 2015-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 1.99 Å R-free 0.254
5B40 The nucleosome structure containing H2B-K120 and H4-K31 monoubiquitinations Deposited 2016-03-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Mutation：C110A Mutation：C110A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；90mM Tris-HCl (pH 7.8), 3.6% PGA-LM, 25.2% PEG 400, 2-6% Pentaerythritol ethoxylate (3/4 EO/OH)
Resolution 3.33 Å R-free 0.263
5BO0 Crystal structure of Human MCM2 HBD and ASF1b chaperoning a histone H3.2-H4 dimer Deposited 2015-05-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 57–136（80 aa） Fragment：UNP residues 57-136
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；3.2 M sodium formate, 0.1 M Tris, pH 8.5
Resolution 2.91 Å R-free 0.238
5VAC Crystal Structure of ATXR5 SET domain in complex with K36me3 histone H3 peptide Deposited 2017-03-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 19–37（19 aa） Fragment：residues 19-37
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；50% polypropylene glycol 400, 5% DMSO, 0.1 M HEPES-NaOH (pH 6.0)
Resolution 1.95 Å R-free 0.228
6FML CryoEM Structure INO80core Nucleosome complex Deposited 2018-01-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM HEPES pH 8, 60 mM KCl, 0.5% glycerol, 0.25 mM CaCl2, 20 uM ZnCl2, 0.25 mM DTT, 0.05% Octyl-beta-glucoside
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.34 Å
6T79 Structure of a human nucleosome at 3.2 A resolution Deposited 2019-10-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 3.20 Å
6T7A Structure of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 3.70 Å
6T7B Structure of human Sox2 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 5.10 Å
6T7C Structure of two copies of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 4.00 Å
6T7D Structure of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 4.40 Å
6X59 The mouse cGAS catalytic domain binding to human assembled nucleosome Deposited 2020-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
6X5A The mouse cGAS catalytic domain binding to human nucleosome that purified from HEK293T cells Deposited 2020-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.36 Å
6XJD Two mouse cGAS catalytic domain binding to human assembled nucleosome Deposited 2020-06-23 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.80 Å
6Y5D Structure of human cGAS (K394E) bound to the nucleosome Deposited 2020-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain A 39–136（98 aa）
Chain E 39–136（98 aa）
Chain M 39–136（98 aa）
Chain Q 39–136（98 aa）
Not recorded PTD PENTANEDIAL × 9 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6Y5E Structure of human cGAS (K394E) bound to the nucleosome (focused refinement of cGAS-NCP subcomplex) Deposited 2020-02-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 39–134（96 aa）
Chain E 39–134（96 aa）
Not recorded PTD PENTANEDIAL × 8 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
7BQZ Crystal Structure of Spindlin1 bound to H3(K4me3-K9me3) peptide Deposited 2020-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–16（15 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；2.8M sodium acetate, pH7.0
Resolution 3.10 Å R-free 0.264
7BQZ Crystal Structure of Spindlin1 bound to H3(K4me3-K9me3) peptide Deposited 2020-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–16（15 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；2.8M sodium acetate, pH7.0
Resolution 3.10 Å R-free 0.264
7BQZ Crystal Structure of Spindlin1 bound to H3(K4me3-K9me3) peptide Deposited 2020-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 2–16（15 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；2.8M sodium acetate, pH7.0
Resolution 3.10 Å R-free 0.264
7BQZ Crystal Structure of Spindlin1 bound to H3(K4me3-K9me3) peptide Deposited 2020-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 2–16（15 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；2.8M sodium acetate, pH7.0
Resolution 3.10 Å R-free 0.264
7BU9 Crystal Structure of Spindlin1-H3(K4me3-K9me2) complex Deposited 2020-04-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–16（15 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；3.6M sodium formate, 3% DMSO
Resolution 3.50 Å R-free 0.264
7BU9 Crystal Structure of Spindlin1-H3(K4me3-K9me2) complex Deposited 2020-04-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–16（15 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；3.6M sodium formate, 3% DMSO
Resolution 3.50 Å R-free 0.264
7BU9 Crystal Structure of Spindlin1-H3(K4me3-K9me2) complex Deposited 2020-04-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 2–16（15 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；3.6M sodium formate, 3% DMSO
Resolution 3.50 Å R-free 0.264
7BU9 Crystal Structure of Spindlin1-H3(K4me3-K9me2) complex Deposited 2020-04-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 2–16（15 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；3.6M sodium formate, 3% DMSO
Resolution 3.50 Å R-free 0.264
7JO9 1:1 cGAS-nucleosome complex Deposited 2020-08-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7JOA 2:1 cGAS-nucleosome complex Deposited 2020-08-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7JZV Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome Deposited 2020-09-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain P 2–136（135 aa）
Chain p 2–136（135 aa）
Mutation：C110A Mutation：C110A ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7PET The 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 34 PDB declaration: 36-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Chain k 1–136（136 aa）
Chain o 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.50 Å
7PEU Trinucleosome of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
7PEV Nucleosome stack of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.00 Å
7PEW Nucleosome 1 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
7PEX Nucleosome 2 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
7PEY Nucleosome 3 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7PEZ Nucleosome 4 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain k 1–136（136 aa）
Chain o 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.90 Å
7PF0 Trinucleosome of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.00 Å
7PF2 Nucleosome stack of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
7PF3 Nucleosome 4 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain k 1–136（136 aa）
Chain o 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7PF4 Nucleosome 3 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7PF5 Nucleosome 2 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7PF6 Nucleosome 1 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7PFA Trinucleosome of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.70 Å
7PFC Nucleosome stack of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
7PFD Nucleosome 1 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7PFE Nucleosome 2 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7PFF Nucleosome 3 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7PFT Trinucleosome of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.80 Å
7PFU Nucleosome stack of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.00 Å
7PFV Nucleosome 1 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7PFW Nucleosome 2 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.20 Å
7PFX Nucleosome 3 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7TAN Structure of VRK1 C-terminal tail bound to nucleosome core particle Deposited 2021-12-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.00 Å
7U50 APE1 bound to a nucleosome core particle with AP-site at SHL-6 Deposited 2022-03-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7U51 Nucleosome core particle with AP-site at SHL-6 Deposited 2022-03-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7U52 nucleosome core particle with AP-site at SHL-6.5 Deposited 2022-03-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7U53 Nucleosome core particle with AP-site at SHL0 Deposited 2022-03-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7UV9 KDM2A-nucleosome structure stabilized by H3K36C-UNC8015 covalent conjugate Deposited 2022-04-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Mutation：K36C Mutation：K36C OH0 N-heptanoyl-N-hydroxy-beta-alanine × 1 FE FE (III) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.20 Å
7UVA Crystal structure of KDM2A histone demethylase catalytic domain in complex with an H3C36 peptide modified by UNC8015 Deposited 2022-04-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 30–42（13 aa） Fragment：UNP residues 30-42
Mutation：K36C FE FE (III) ION × 1 OH0 N-heptanoyl-N-hydroxy-beta-alanine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；100 mM Tris-Cl, pH 8.5, 150 mM lithium sulfate, 20% PEG3350
Resolution 1.98 Å R-free 0.237
7UVA Crystal structure of KDM2A histone demethylase catalytic domain in complex with an H3C36 peptide modified by UNC8015 Deposited 2022-04-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 30–42（13 aa） Fragment：UNP residues 30-42
Mutation：K36C FE FE (III) ION × 1 OH0 N-heptanoyl-N-hydroxy-beta-alanine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；100 mM Tris-Cl, pH 8.5, 150 mM lithium sulfate, 20% PEG3350
Resolution 1.98 Å R-free 0.237
8ATF Nucleosome-bound Ino80 ATPase Deposited 2022-08-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.45 Å
8AV6 CryoEM structure of INO80 core nucleosome complex in closed grappler conformation Deposited 2022-08-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.68 Å
8JLB Cryo-EM structure of the 145 bp human nucleosome containing H3.2 C110A mutant Deposited 2023-06-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Mutation：C110A Mutation：C110A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.36 Å
8JLD Cryo-EM structure of the 145 bp human nucleosome containing acetylated H3 tail Deposited 2023-06-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Mutation：C110A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C110A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.48 Å
8OL1 cGAS-Nucleosome in complex with SPSB3-ELOBC (composite structure) Deposited 2023-03-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 38–135（98 aa）
Chain E 38–135（98 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；PBS buffer
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8VMJ H3K4me3 nucleosome bound to PRC2_AJ119-450 Deposited 2024-01-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain I 1–136（136 aa）
Chain O 1–136（136 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8VMN H3K4me3 nucleosome bound to PRC2_AJ1-450 Deposited 2024-01-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain I 1–136（136 aa）
Chain O 1–136（136 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8VO0 H3K36me3-modified nucleosome bound to PRC2_AJ1-450 with histone H3 tail disengaged Deposited 2024-01-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain I 42–136（95 aa）
Chain O 42–136（95 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8VOB H3K36me3-modified nucleosome bound to PRC2_AJ1-450 Deposited 2024-01-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain I 1–136（136 aa）
Chain O 1–136（136 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8VWS Nucleosome containing 8oxoG at SHL-6 Deposited 2024-02-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；50 mM HEPES (pH-7.1), 100 mM NaCl, 1 mM TCEP, and 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8VWT OGG1 bound to a nucleosome containing 8oxoG at SHL-6 (composite map) Deposited 2024-02-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；50 mM HEPES (pH-7.1), 100 mM NaCl, 1 mM TCEP, and 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8VWU Nucleosome containing 8oxoG at SHL4 Deposited 2024-02-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；50 mM HEPES (pH-7.1), 100 mM NaCl, 1 mM TCEP, and 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8VWV OGG1 bound to a nucleosome containing 8oxoG at SHL4 (composite map) Deposited 2024-02-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；50 mM HEPES (pH-7.1), 100 mM NaCl, 1 mM TCEP, and 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8X7I Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by intein-based E2-Ub-NCP conjugation strategy Deposited 2023-11-24 Different construct Different oligomeric state Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 38–135（98 aa）
Chain E 38–135（98 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
8X7J Cryo-EM structures of RNF168/UbcH5c-Ub/nucleosomes complex determined by activity-based chemical trapping strategy Deposited 2023-11-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 39–135（97 aa）
Chain E 39–135（97 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
8ZJR Structure of nucleosome-bound RFX5 complex Deposited 2024-05-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8ZJT Structure of free nucleosome Deposited 2024-05-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9BE5 Cryo-EM structure of Human Nucleosome collected by EPU on Glacios at 3.3 Angstrom resolution Deposited 2024-04-14 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 39–135（97 aa）
Chain E 39–136（98 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9BE6 Cryo-EM structure of Human Nucleosome collected by Leginon on Krios at 3.0 Angstrom resolution Deposited 2024-04-14 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 39–135（97 aa）
Chain E 40–136（97 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9D3K Two Dsup molecules in complex with the nucleosome open from both sides Deposited 2024-08-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 42–136（95 aa）
Chain E 42–136（95 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
9D3L Two Dsup molecules in complex with the nucleosome open from the left side Deposited 2024-08-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 39–136（98 aa）
Chain E 39–136（98 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9D3M Two HMGN2s in complex with the nucleosome Deposited 2024-08-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 38–136（99 aa）
Chain E 38–136（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9D3N 167-bp 5S rDNA nucleosome cross-linked with glutaraldehyde Deposited 2024-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 45–134（90 aa）
Chain E 45–134（90 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9D3O 167-bp 5S rDNA nucleosome - closed Deposited 2024-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 38–136（99 aa）
Chain E 38–136（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9D3P 167-bp 5S rDNA nucleosome - open I (open only on the downstream side) Deposited 2024-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 38–136（99 aa）
Chain E 38–136（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
9D3Q 167-bp 5S rDNA nucleosome - open II Deposited 2024-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 41–136（96 aa）
Chain E 41–136（96 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9D3R 147-bp 5S rDNA nucleosome - closed Deposited 2024-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 40–136（97 aa）
Chain E 40–136（97 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9D3S 147-bp 5S rDNA nucleosome - open I (open on the downstream side) Deposited 2024-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 38–136（99 aa）
Chain E 38–136（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9D3T 147-bp 5S rDNA nucleosome cross-linked with glutaraldehyde Deposited 2024-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 44–136（93 aa）
Chain E 44–136（93 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9DWF Nucleosome containing a 1-nt gap at SHL-4.5 Deposited 2024-10-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9DWG DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 1, composite) Deposited 2024-10-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9DWH DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 2, composite) Deposited 2024-10-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9DWI DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 3, composite) Deposited 2024-10-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9DWJ Nucleosome containing a 1-nt gap at SHL-3.5 Deposited 2024-10-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9DWK DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-3.5 Deposited 2024-10-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: dodecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
9DWL Nucleosome containing a 1-nt gap at SHL-5.5 Deposited 2024-10-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
9DWM DNA polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-5.5 Deposited 2024-10-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: dodecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9E00 Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Deposited 2024-10-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Not recorded ZN ZINC ION × 9 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.75 Å
9E05 The consensus model of the cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Deposited 2024-10-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.00 Å
9E09 Cryo-EM structure a single nucleosome (2) focus of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Deposited 2024-10-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.72 Å
9E0R Cryo-EM structure of a single nucleosome (1) focus of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Deposited 2024-10-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9E2D Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to a di-nucleosome with a five base pair linker Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.08 Å
9E2F Cryo-EM structure of a di-nucleosome with a five base pair linker Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.90 Å
9E2Q Cryo-EM structure of DNMT 3A2/3B3 tetramer in complex with a di-nucleosome with a six base pair linker Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.14 Å
9E2R Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to a di-nucleosome and an histone-3 peptide Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.71 Å
9E3D Cryo-EM structure of DNMT 3A2/3B3 tetramer in complex with a di-nucleosome with K120R mutant H2B Deposited 2024-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Not recorded ZN ZINC ION × 9 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9E3R Cryo-EM structure of PWWP domain deleted DNMT 3A2/3B3 in complex with a di-nucleosome Deposited 2024-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
9E3U Cryo-EM structure of DNMT 3A2/3B3 tetramer bound to a di-nucleosome with a 25 base-pair linker Deposited 2024-10-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded ZN ZINC ION × 9 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.90 Å
9E49 Cryo-EM structure of a di-nucleosome with an eight base-pair linker Deposited 2024-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.93 Å
9GMK SIRT7:H3K18DTU nucleosome complex Deposited 2024-08-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9GMR SIRT7-H3K36MTUnucleosome complex Deposited 2024-08-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded A1IY0 [[(2~{R},3~{a}~{R},5~{R},6~{R},6~{a}~{R})-2-(methylamino)-6-oxidanyl-2-(propylamino)-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxathiol-5-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9GW2 State 2 MAP 1 SETD2 bound to proximal H3 of upstream nucleosome Deposited 2024-09-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.84 Å
9IPU cryo-EM structure of the RNF168(1-193)/UbcH5c-Ub ubiquitylation module bound to H1.0-K63-Ub3 modified chromatosome Deposited 2024-07-11 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
9NQU KDM6B-nucleosome structure stabilized by H3K27C-UNC8015 covalent conjugate Deposited 2025-03-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded FE FE (III) ION × 1 ZN ZINC ION × 1 OH0 N-heptanoyl-N-hydroxy-beta-alanine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.16 Å
9OGR Cryo-EM analysis of human H2A.Z on methylated Sat2R-P DNA (v1) Deposited 2025-05-01 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.78 Å
9OGS Cryo-EM analysis of human H2A.Z on Sat2R-P DNA (v1) Deposited 2025-05-01 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
9OGZ Cryo-EM analysis of human H2A.Z on Sat2R-P DNA (v2) Deposited 2025-05-02 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
9OH0 Cryo-EM analysis of human H2A.Z on methylated Sat2R-P DNA (v2) Deposited 2025-05-02 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.78 Å
9OH1 Cryo-EM analysis of human H2A.Z on 601L DNA Deposited 2025-05-02 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
9OH2 Cryo-EM analysis of human H2A.Z on methylated 601L DNA Deposited 2025-05-02 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.14 Å
9RZC State 3 MAP 1 SETD2 bound to distal H3 of upstream nucleosome Deposited 2025-07-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.66 Å
9RZE State 2 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to proximal upstream H3 Deposited 2025-07-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.53 Å
9S0U State 3 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to distal upstream H3 Deposited 2025-07-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.72 Å
9S3G State 1 MAP3 RNA Pol II activated elongation complex with SETD2 and upstream hexasome Deposited 2025-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
9U5U The 1:1 cryo-EM structure of BAP1/ASXL1-K351Ub in complex with H2AK119Ub nucleosome Deposited 2025-03-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
9Y46 Human nucleosome structure on Nickel-NTA lipid affinity grid (C2 refinement) Deposited 2025-09-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.59 Å
9Y47 Human nucleosome structure on Nickel-NTA lipid affinity grid (C1 refinement) Deposited 2025-09-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.74 Å
9ZEN Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1B2 Deposited 2025-11-30 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain A 39–135（97 aa）
Chain E 39–135（97 aa）
Mutation：C97S Mutation：C97S No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES pH7.6, 50 mM NaCl, 0.5 mM MgCl2, 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.17 Å

139 other PDB entries and 157 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H32_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–97； UniProt 39–135 Author chain E； PDBConstruct 1–97； UniProt 39–135

Histone H4

Homo sapiens

UniProt P62805

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 10 DNA 2 PDB declaration: dodecameric（12） Consistent with all polymer counts Chain B； UniProt 21–102 Chain F； UniProt 21–102 Not recorded Histone H3.2 × 2 （Q71DI3） Histone H2A type 1-B/E × 1 （P04908） Histone H2B type 1-K × 2 （O60814） Histone H2A type 1-B/E × 1 （P04908） DNA (143-MER) × 1 DNA (143-MER) × 1 Ubiquitin-conjugating enzyme E2 D3 × 1 （P61077） E3 ubiquitin-protein ligase RNF168 × 1 （Q8IYW5） ZN ZINC ION × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.27 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8X7K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
10XZ Non-damaged nucleosome Deposited 2026-02-12 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
10YA Nucleosome containing a nick at SHL-4 Deposited 2026-02-12 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
10YB Nucleosome containing a nick at SHL-2 Deposited 2026-02-12 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
10YC Nucleosome containing a nick at SHL-4 Deposited 2026-02-12 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
10YD Nucleosome containing a nick at SHL-6 Deposited 2026-02-12 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
10YE DNA Ligase IIIa bound to nucleosome containing a nick at SHL0 Deposited 2026-02-12 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain B 23–102（80 aa）
Chain F 23–102（80 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
10YF DNA Ligase IIIa bound to nucleosome containing a nick at SHL-2 (composite) Deposited 2026-02-12 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain B 23–102（80 aa）
Chain F 23–102（80 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution not provided
10YG DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-4 (composite) Deposited 2026-02-12 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain B 23–102（80 aa）
Chain F 23–102（80 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution not provided
10YH DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-6 (composite) Deposited 2026-02-12 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain B 23–102（80 aa）
Chain F 23–102（80 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
10YI XRCC1-DNA Ligase IIIa complex bound to a nucleosome containing a nick at SHL-6 (composite) Deposited 2026-02-12 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain B 23–102（80 aa）
Chain F 23–102（80 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
2BQZ Crystal structure of a ternary complex of the human histone methyltransferase Pr-SET7 (also known as SET8) Deposited 2005-04-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 17–25（9 aa） Fragment：RESIDUES 17-25
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.00
Resolution 1.50 Å R-free 0.206
2BQZ Crystal structure of a ternary complex of the human histone methyltransferase Pr-SET7 (also known as SET8) Deposited 2005-04-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 17–25（9 aa） Fragment：RESIDUES 17-25
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.00
Resolution 1.50 Å R-free 0.206
2CV5 Crystal structure of human nucleosome core particle Deposited 2005-05-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 0–102（103 aa）
Chain F 0–102（103 aa）
Not recorded MN MANGANESE (II) ION × 9 CL CHLORIDE ION × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.277
2LVM Solution structure of human 53BP1 tandem Tudor domains in complex with a histone H4K20me2 peptide Deposited 2012-07-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 15–28（14 aa） Fragment：UNP residues 15-28
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 1.7 mM [U-100% 13C; U-100% 15N] protein_1, 8.5 mM protein_2, 25 mM sodium phosphate, 0.001 % DSS, 0.001 % NaN3, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.7 mM [U-100% 13C; U-100% 15N] protein_1, 8.5 mM protein_2, 25 mM sodium phosphate, 0.001 % DSS, 0.001 % NaN3, 100% D2O | 100% D2O
NMR sample composition 5 mM protein_1, 4 mM [U-100% 13C; U-100% 15N] protein_2, 25 mM sodium phosphate, 0.001 % DSS, 0.001 % NaN3, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 5 mM protein_1, 4 mM [U-100% 13C; U-100% 15N] protein_2, 25 mM sodium phosphate, 0.001 % DSS, 0.001 % NaN3, 100% D2O | 100% D2O
Resolution not provided
2RNY Complex Structures of CBP Bromodomain with H4 ack20 Peptide Deposited 2008-02-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 14–28（15 aa） Fragment：UNP residues 14-28
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient
NMR sample composition 0.5mM [U-100% 13C; U-100% 15N] sodium phosphate, 100% D2O | 100% D2O
Resolution not provided
2RS9 Solution structure of the bromodomain of human BRPF1 in complex with histone H4K5ac peptide Deposited 2011-12-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–11（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；288 K；Ionic strength (raw mmCIF value) 100；Pressure ambient
NMR sample composition 1.5 mM H4K5ac-1, 0.54 mM [U-99% 13C; U-99% 15N] Bromodomain-2, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
3A6N The nucleosome containing a testis-specific histone variant, human H3T Deposited 2009-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.70 Å R-free 0.264
3AFA The human nucleosome structure Deposited 2010-02-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.270
3AV1 The human nucleosome structure containing the histone variant H3.2 Deposited 2011-02-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.290
3AV2 The human nucleosome structure containing the histone variant H3.3 Deposited 2011-02-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.272
3AYW Crystal Structure of Human Nucleosome Core Particle Containing H3K56Q mutation Deposited 2011-05-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.90 Å R-free 0.273
3AZE Crystal Structure of Human Nucleosome Core Particle Containing H3K64Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.00 Å R-free 0.302
3AZF Crystal Structure of Human Nucleosome Core Particle Containing H3K79Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.70 Å R-free 0.263
3AZG Crystal Structure of Human Nucleosome Core Particle Containing H3K115Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.40 Å R-free 0.269
3AZH Crystal Structure of Human Nucleosome Core Particle Containing H3K122Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 3 MN MANGANESE (II) ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.49 Å R-free 0.266
3AZI Crystal Structure of Human Nucleosome Core Particle Containing H4K31Q mutation Deposited 2011-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Mutation：K31Q Mutation：K31Q CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.70 Å R-free 0.289
3AZJ Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q mutation Deposited 2011-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Mutation：K44Q Mutation：K44Q CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.89 Å R-free 0.268
3AZK Crystal Structure of Human Nucleosome Core Particle Containing H4K59Q mutation Deposited 2011-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Mutation：K59Q Mutation：K59Q CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.20 Å R-free 0.258
3AZL Crystal Structure of Human Nucleosome Core Particle Containing H4K77Q mutation Deposited 2011-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Mutation：K77Q Mutation：K77Q CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.70 Å R-free 0.259
3AZM Crystal Structure of Human Nucleosome Core Particle Containing H4K79Q mutation Deposited 2011-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Mutation：K79Q Mutation：K79Q CL CHLORIDE ION × 3 MN MANGANESE (II) ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.89 Å R-free 0.296
3AZN Crystal Structure of Human Nucleosome Core Particle Containing H4K91Q mutation Deposited 2011-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Mutation：K91Q Mutation：K91Q CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.00 Å R-free 0.254
3CFS Structural basis of the interaction of RbAp46/RbAp48 with histone H4 Deposited 2008-03-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 28–42（15 aa） Fragment：UNP residues 28 to 42
Not recorded ARS ARSENIC × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；277 K；18% PEG8000, 0.2M Ca acetate, 0.1M Na Cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.40 Å R-free 0.249
3CFV Structural basis of the interaction of RbAp46/RbAp48 with histone H4 Deposited 2008-03-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 25–42（18 aa） Fragment：UNP residues 25 to 42
Not recorded ARS ARSENIC × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；277 K；13% PEG 2000, 0.2M Ca acetate, 0.1M Na Cacodylate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.60 Å R-free 0.257
3CFV Structural basis of the interaction of RbAp46/RbAp48 with histone H4 Deposited 2008-03-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 25–42（18 aa） Fragment：UNP residues 25 to 42
Not recorded ARS ARSENIC × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；277 K；13% PEG 2000, 0.2M Ca acetate, 0.1M Na Cacodylate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.60 Å R-free 0.257
3F9W Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20 / AdoHcy Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 16–25（10 aa） Fragment：UNP residues 16-25
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.60 Å R-free 0.206
3F9W Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20 / AdoHcy Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 16–25（10 aa） Fragment：UNP residues 16-25
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.60 Å R-free 0.206
3F9W Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20 / AdoHcy Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 16–25（10 aa） Fragment：UNP residues 16-25
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.60 Å R-free 0.206
3F9W Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20 / AdoHcy Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 16–25（10 aa） Fragment：UNP residues 16-25
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.60 Å R-free 0.206
3F9X Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20me2 / AdoHcy Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 16–25（10 aa） Fragment：UNP residues 16-25
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.25 Å R-free 0.207
3F9X Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20me2 / AdoHcy Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 16–25（10 aa） Fragment：UNP residues 16-25
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.25 Å R-free 0.207
3F9X Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20me2 / AdoHcy Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 16–25（10 aa） Fragment：UNP residues 16-25
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.25 Å R-free 0.207
3F9X Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20me2 / AdoHcy Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 16–25（10 aa） Fragment：UNP residues 16-25
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.25 Å R-free 0.207
3F9Y Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20me1 / AdoHcy Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 16–25（10 aa） Fragment：UNP residues 16-25
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.50 Å R-free 0.220
3F9Y Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20me1 / AdoHcy Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 16–25（10 aa） Fragment：UNP residues 16-25
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.50 Å R-free 0.220
3F9Z Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y245F / H4-Lys20 / AdoHcy Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 16–25（10 aa） Fragment：UNP residues 16-25
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.60 Å R-free 0.257
3F9Z Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y245F / H4-Lys20 / AdoHcy Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 16–25（10 aa） Fragment：UNP residues 16-25
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.60 Å R-free 0.257
3F9Z Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y245F / H4-Lys20 / AdoHcy Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 16–25（10 aa） Fragment：UNP residues 16-25
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.60 Å R-free 0.257
3F9Z Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y245F / H4-Lys20 / AdoHcy Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 16–25（10 aa） Fragment：UNP residues 16-25
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.60 Å R-free 0.257
3NQJ Crystal structure of (CENP-A/H4)2 heterotetramer Deposited 2010-06-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 21–103（83 aa） Fragment：UNP residues 21-103
Not recorded PO4 PHOSPHATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.17 M ammonium sulfate, 0.085 M sodium cacodylate (pH 6.5), 25.5% PEG-8000, 15% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.10 Å R-free 0.241
3NQU Crystal structure of partially trypsinized (CENP-A/H4)2 heterotetramer Deposited 2010-06-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–103（103 aa）
Not recorded SO4 SULFATE ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；295 K；2 M ammonium sulfate, 0.1 M HEPES (pH 7.9), VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.50 Å R-free 0.302
3O36 Crystal structure of TRIM24 PHD-Bromo complexed with H4(14-19)K16ac peptide Deposited 2010-07-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 15–20（6 aa） Fragment：UNP residues 15-20
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；50 mM Bis-Tris (pH 6.5), 30% Polyethylene glycol 3350, 100 mM ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.70 Å R-free 0.216
3O36 Crystal structure of TRIM24 PHD-Bromo complexed with H4(14-19)K16ac peptide Deposited 2010-07-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 15–20（6 aa） Fragment：UNP residues 15-20
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；50 mM Bis-Tris (pH 6.5), 30% Polyethylene glycol 3350, 100 mM ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.70 Å R-free 0.216
3QZS Crystal Structure of BPTF bromo in complex with histone H4K16ac - Form I Deposited 2011-03-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 13–22（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；100 mM Tris-HCl pH 8.0, 20% Glycerol, vapor diffusion, hanging drop
Resolution 1.80 Å R-free 0.230
3QZS Crystal Structure of BPTF bromo in complex with histone H4K16ac - Form I Deposited 2011-03-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 13–22（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；100 mM Tris-HCl pH 8.0, 20% Glycerol, vapor diffusion, hanging drop
Resolution 1.80 Å R-free 0.230
3QZT Crystal Structure of BPTF bromo in complex with histone H4K16ac - Form II Deposited 2011-03-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 13–22（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；20% (W/V) PEGMME 2K, 20% Glycerol and 0.2 M KCl, 0.1 M Tris-HCL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.50 Å R-free 0.198
3QZV Crystal Structure of BPTF PHD-linker-bromo in complex with histone H4K12ac peptide Deposited 2011-03-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 8–18（11 aa） Fragment：Histone H4 7-17
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20% (W/V) PEG3000, 0.3 M NaAcetate, 0.1 M Na-Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.00 Å R-free 0.234
3R45 Structure of a CENP-A-Histone H4 Heterodimer in complex with chaperone HJURP Deposited 2011-03-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–103（103 aa）
Not recorded SO4 SULFATE ION × 13 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；2M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.60 Å R-free 0.245
3UVW Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H4K5acK8ac) Deposited 2011-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–12（11 aa） Fragment：unp residues 2-12
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；278 K；0.1M Tris, 20% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 278K, pH 8.0
Resolution 1.37 Å R-free 0.171
3UVY Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H4K16acK20ac) Deposited 2011-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 16–26（11 aa） Fragment：UNP RESIDUES 16-26
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；278 K；0.2M NaI, 0.1M BTProp, 20% PEG 3350, 10% EtGly, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K
Resolution 2.02 Å R-free 0.258
3UW9 Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H4K8acK12ac) Deposited 2011-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 8–18（11 aa） Fragment：unp residues 8-18
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.1M Tris, 0.3M LiCl 15% PEG6000, 10% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 8.0
Resolution 2.30 Å R-free 0.257
3UW9 Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H4K8acK12ac) Deposited 2011-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 8–18（11 aa） Fragment：unp residues 8-18
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.1M Tris, 0.3M LiCl 15% PEG6000, 10% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 8.0
Resolution 2.30 Å R-free 0.257
3W96 Crystal Structure of Human Nucleosome Core Particle lacking H2A N-terminal region Deposited 2013-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 1 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.00 Å R-free 0.296
3W97 Crystal Structure of Human Nucleosome Core Particle lacking H2B N-terminal region Deposited 2013-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.20 Å R-free 0.321
3W98 Crystal Structure of Human Nucleosome Core Particle lacking H3.1 N-terminal region Deposited 2013-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.42 Å R-free 0.303
3W99 Crystal Structure of Human Nucleosome Core Particle lacking H4 N-terminal region Deposited 2013-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 17–103（87 aa） Fragment：UNP residues 17-103
Chain F 17–103（87 aa） Fragment：UNP residues 17-103
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.00 Å R-free 0.312
3WA9 The nucleosome containing human H2A.Z.1 Deposited 2013-04-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.07 Å R-free 0.271
3WAA The nucleosome containing human H2A.Z.2 Deposited 2013-04-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.20 Å R-free 0.271
3WKJ The nucleosome containing human TSH2B Deposited 2013-10-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.291
3WTP Crystal Structure of the heterotypic nucleosome containing human CENP-A and H3.3 Deposited 2014-04-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, vapor diffusion, hanging drop, temperature 293K
Resolution 2.67 Å R-free 0.270
3X1S Crystal structure of the nucleosome core particle Deposited 2014-11-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded MN MANGANESE (II) ION × 6 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；60-70mM KCL, 70-90mM MnCl2, 24% MPD, 20mM Na-Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.81 Å R-free 0.270
3X1T Crystal structure of nucleosome core particle consisting of mouse testis specific histone variants H2aa and H2ba Deposited 2014-11-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded MN MANGANESE (II) ION × 22 CL CHLORIDE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；60-70mM Kcl, 70-90mM MnCl2, 24% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.81 Å R-free 0.266
3X1U Crystal structure of nucleosome core particle in the presence of histone variants involved in reprogramming Deposited 2014-11-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded MN MANGANESE (II) ION × 4 CL CHLORIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；60-70 mM KCl, 70-90 mM MnCl2, 24% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.25 Å R-free 0.270
3X1V Crystal structure of nucleosome core particle in the presence of histone variant involved in reprogramming Deposited 2014-11-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded MN MANGANESE (II) ION × 19 CL CHLORIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；60-70 mM KCl, 70-90 mM MnCl2, Na-cocodylate, 24% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.92 Å R-free 0.259
4GQB Crystal Structure of the human PRMT5:MEP50 Complex Deposited 2012-08-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain C 2–22（21 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 0XU (2S,5S,6E)-2,5-diamino-6-[(3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxydihydrofuran-2(3H)-ylidene]hexanoic acid × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20-30% PEG3350, 100-250 mM ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.06 Å R-free 0.222
4H9N Complex structure 1 of DAXX/H3.3(sub5)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–103（102 aa）
Not recorded PO4 PHOSPHATE ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1.8 M Na/K-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.95 Å R-free 0.209
4H9O Complex structure 2 of DAXX/H3.3(sub5,G90M)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–103（102 aa）
Not recorded PO4 PHOSPHATE ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1.8 M Na/K-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.05 Å R-free 0.225
4H9P Complex structure 3 of DAXX/H3.3(sub5,G90A)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–103（102 aa）
Not recorded PO4 PHOSPHATE ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；1.8 M Na/K-phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.20 Å R-free 0.242
4H9P Complex structure 3 of DAXX/H3.3(sub5,G90A)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 2–103（102 aa）
Not recorded PO4 PHOSPHATE ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；1.8 M Na/K-phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.20 Å R-free 0.242
4H9Q Complex structure 4 of DAXX(E225A)/H3.3(sub5)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–103（102 aa）
Not recorded PO4 PHOSPHATE ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1.8 M Na/K-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.95 Å R-free 0.221
4H9Q Complex structure 4 of DAXX(E225A)/H3.3(sub5)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 2–103（102 aa）
Not recorded PO4 PHOSPHATE ION × 18 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1.8 M Na/K-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.95 Å R-free 0.221
4H9R Complex structure 5 of DAXX(E225A)/H3.3(sub5,G90A)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–103（102 aa）
Not recorded PO4 PHOSPHATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；1.6 M Na/K-phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.20 Å R-free 0.230
4H9R Complex structure 5 of DAXX(E225A)/H3.3(sub5,G90A)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 2–103（102 aa）
Not recorded PO4 PHOSPHATE ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；1.6 M Na/K-phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.20 Å R-free 0.230
4H9S Complex structure 6 of DAXX/H3.3(sub7)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 21–103（83 aa）
Not recorded PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；0.1 M Na/K-phosphate, 2.5M NaCl, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.250
4H9S Complex structure 6 of DAXX/H3.3(sub7)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 21–103（83 aa）
Not recorded PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；0.1 M Na/K-phosphate, 2.5M NaCl, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.250
4H9S Complex structure 6 of DAXX/H3.3(sub7)/H4 Deposited 2012-09-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 21–103（83 aa）
Chain D 21–103（83 aa）
Not recorded PO4 PHOSPHATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；0.1 M Na/K-phosphate, 2.5M NaCl, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.250
4HGA Structure of the variant histone H3.3-H4 heterodimer in complex with its chaperone DAXX Deposited 2012-10-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–103（103 aa）
Not recorded PC4 TETRACHLOROPLATINATE(II) × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；298 K；0.1M HEPES-Na, pH 7.6, 23% (v/v) PEG 3350, 0.25M Ammonium acetate, 1% Tacsimate pH 7.0, 6% ethanol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.80 Å R-free 0.271
4M38 Crystal structure of Trypanosoma brucei protein arginine methyltransferase 7 complex with AdoHcy and histone H4 peptide Deposited 2013-08-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 2–22（21 aa） Fragment：UNP residues 2-22
Chain F 2–22（21 aa） Fragment：UNP residues 2-22
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；100mM MES, 20% PEG 1000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.230
4QUT Structure of the bromodomain of human ATPase family AAA domain-containing protein 2 (ATAD2) complexed with Histone H4-K(ac)12 Deposited 2014-07-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 7–13（7 aa） Fragment：histone H4 tail
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277.15 K；apo crystals grew in 1.8-2.2 M ammonium sulphate, 0.1 M Bis-Tris, pH 5.5-6.5. Soaking performed in 28-32% PEG 3350, 50 mM bis-tris pH 5.5, 50 mM ammonium phosphate and 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Resolution 1.70 Å R-free 0.180
4QUU Structure of the bromodomain of human ATPase family AAA domain-containing protein 2 (ATAD2) complexed with Histone H4-K(ac)5 Deposited 2014-07-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–13（13 aa） Fragment：histone H4 tail
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277.15 K；apo crystals grew in 1.8-2.2 M ammonium sulphate, 0.1 M Bis-Tris, pH 5.5-6.5. Soaking performed in 28-32% PEG 3350, 50 mM bis-tris pH 5.5, 50 mM ammonium phosphate and 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Resolution 1.80 Å R-free 0.200
4QYD Crystal Structure of the human BRPF1 bromodomain in complex with a histone H4K12ac peptide Deposited 2014-07-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 5–18（14 aa） Fragment：histone H4K12ac peptide (UNP residues 5-18)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；277 K；0.1 M HEPES, pH 7.5, 10% w/v polyethylene glycol (PEG) 6,000, 5% v/v (+/-)-2-methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.94 Å R-free 0.213
4YM5 Crystal structure of the human nucleosome containing 6-4PP (inside) Deposited 2015-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 4.00 Å R-free 0.289
4YM6 Crystal structure of the human nucleosome containing 6-4PP (outside) Deposited 2015-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 3.51 Å R-free 0.287
4YY6 Crystal structure of BRD9 Bromodomain bound to a butyryllysine peptide Deposited 2015-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain Z 2–12（11 aa） Fragment：N-terminal tail (UNP residues 2-12)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；277 K；0.2 M sodium malonate, pH 4.0, 20% w/v PEG3350
Resolution 1.45 Å R-free 0.208
4YYD Crystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide Deposited 2015-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain Z 2–12（11 aa） Fragment：N-terminal tail (UNP residues 2-12)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2 M sodium malonate, pH 7.0, 20% w/v PEG3350
Resolution 1.52 Å R-free 0.226
4YYG Crystal structure of BRD9 Bromodomain bound to a butyryllysine peptide Deposited 2015-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–12（11 aa） Fragment：N-terminal tail (UNP residues 2-12)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.05 M calcium chloride dihydrate, 0.1 M Bis-Tris, pH 6.5, 30% v/v PEG550 MME
Resolution 2.10 Å R-free 0.311
4YYH Crystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide Deposited 2015-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain Z 2–12（11 aa） Fragment：N-terminal tail (UNP residues 2-12)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1 M sodium citrate, pH 5.5, 0.2 M sodium chloride, 20% w/v PEG3350
Resolution 1.74 Å R-free 0.260
4YYH Crystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide Deposited 2015-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain Y 2–12（11 aa） Fragment：N-terminal tail (UNP residues 2-12)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1 M sodium citrate, pH 5.5, 0.2 M sodium chloride, 20% w/v PEG3350
Resolution 1.74 Å R-free 0.260
4YYI Crystal structure of BRD9 Bromodomain bound to an acetylated peptide Deposited 2015-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 2–12（11 aa） Fragment：N-terminal tail (UNP residues 2-12)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1 M Bis-Tris, pH 6.5, 25% w/v PEG3350
Resolution 1.50 Å R-free 0.242
4YYI Crystal structure of BRD9 Bromodomain bound to an acetylated peptide Deposited 2015-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 2–12（11 aa） Fragment：N-terminal tail (UNP residues 2-12)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1 M Bis-Tris, pH 6.5, 25% w/v PEG3350
Resolution 1.50 Å R-free 0.242
4YYJ Crystal structure of BRD9 Bromodomain bound to a butyryllysine peptide Deposited 2015-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 2–12（11 aa） Fragment：N-terminal tail (UNP residues 2-12)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M ammonium chloride, 20% w/v PEG3350
Resolution 1.85 Å R-free 0.244
4YYJ Crystal structure of BRD9 Bromodomain bound to a butyryllysine peptide Deposited 2015-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 2–12（11 aa） Fragment：N-terminal tail (UNP residues 2-12)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M ammonium chloride, 20% w/v PEG3350
Resolution 1.85 Å R-free 0.244
4YYK Crystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide Deposited 2015-03-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 2–12（11 aa） Fragment：N-terminal tail (UNP residues 2-12)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1 M MES, pH 6.5, 15% w/v PEG550 MME
Resolution 1.79 Å R-free 0.261
4YYK Crystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide Deposited 2015-03-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 2–12（11 aa） Fragment：N-terminal tail (UNP residues 2-12)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1 M MES, pH 6.5, 15% w/v PEG550 MME
Resolution 1.79 Å R-free 0.261
4YYM Crystal structure of TAF1 BD2 Bromodomain bound to a butyryllysine peptide Deposited 2015-03-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain Z 2–12（11 aa） Fragment：N-terminal tail (UNP residues 2-12)
Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M calcium chloride, 20 w/v PEG3350
Resolution 1.50 Å R-free 0.261
4YYN Crystal structure of TAF1 BD2 Bromodomain bound to a crotonyllysine peptide Deposited 2015-03-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain Z 2–12（11 aa） Fragment：N-terminal tail (UNP residues 2-12)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M calcium acetate, 20% w/v PEG3350
Resolution 1.85 Å R-free 0.243
4Z2M Crystal structure of human SPT16 Mid-AID/H3-H4 tetramer FACT Histone complex Deposited 2015-03-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain H 1–103（103 aa）
Chain J 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；10% PEG400, 0.9-1.1 M Imidazole, 100-150 mM L-histidine
Resolution 2.98 Å R-free 0.246
4Z5T The nucleosome containing human H3.5 Deposited 2015-04-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.80 Å R-free 0.269
5AV5 human nucleosome core particle Deposited 2015-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions LIQUID DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.40 Å R-free 0.233
5AV6 human nucleosome core particle Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.20 Å R-free 0.229
5AV8 human nucleosome core particle Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.20 Å R-free 0.233
5AV9 human nucleosome core particle Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.20 Å R-free 0.239
5AVB human nucleosome core particle Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.40 Å R-free 0.236
5AVC human nucleosome core particle Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.40 Å R-free 0.238
5AY8 Crystal structure of human nucleosome containing H3.Y Deposited 2015-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 8 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；sodium acetate, manganese chloride, 2-propanol, trimethylamine N-oxide
Resolution 2.80 Å R-free 0.249
5B0Y Crystal structure of the nucleosome containing histone H3 with the crotonylated lysine 122 Deposited 2015-11-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.56 Å R-free 0.249
5B0Z The crystal structure of the nucleosome containing H3.2, at 1.98 A resolution Deposited 2015-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 1.99 Å R-free 0.254
5B24 The crystal structure of the nucleosome containing cyclobutane pyrimidine dimer Deposited 2015-12-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 3.60 Å R-free 0.249
5B2I Human nucleosome containing CpG unmethylated DNA Deposited 2016-01-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 3.00 Å R-free 0.257
5B2J Human nucleosome containing CpG methylated DNA Deposited 2016-01-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.60 Å R-free 0.252
5B31 The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.1. Deposited 2016-02-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 8 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.20 Å R-free 0.271
5B32 The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.3. Deposited 2016-02-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.35 Å R-free 0.259
5B33 The crystal structure of the H2AZ nucleosome with H3.3. Deposited 2016-02-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.92 Å R-free 0.252
5B40 The nucleosome structure containing H2B-K120 and H4-K31 monoubiquitinations Deposited 2016-03-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Mutation：K31C Mutation：K31C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；90mM Tris-HCl (pH 7.8), 3.6% PGA-LM, 25.2% PEG 400, 2-6% Pentaerythritol ethoxylate (3/4 EO/OH)
Resolution 3.33 Å R-free 0.263
5BNV Crystal structure of Human MCM2 HBD chaperoning a histone H3-H4 tetramer Deposited 2015-05-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 2–103（102 aa）
Chain E 2–103（102 aa）
Not recorded PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；1.5 M sodium/potassium phosphate, pH 8.0
Resolution 2.79 Å R-free 0.220
5BNX Crystal structure of Human MCM2 HBD and ASF1b chaperoning a histone H3.3-H4 dimer Deposited 2015-05-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 2–103（102 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；3.2 M sodium formate, 0.1 M Tris, pH 8.5
Resolution 2.31 Å R-free 0.213
5BO0 Crystal structure of Human MCM2 HBD and ASF1b chaperoning a histone H3.2-H4 dimer Deposited 2015-05-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 2–103（102 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；3.2 M sodium formate, 0.1 M Tris, pH 8.5
Resolution 2.91 Å R-free 0.238
5C3I Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2 Deposited 2015-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain K 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0
Resolution 3.50 Å R-free 0.253
5C3I Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2 Deposited 2015-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0
Resolution 3.50 Å R-free 0.253
5C3I Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2 Deposited 2015-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain G 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0
Resolution 3.50 Å R-free 0.253
5C3I Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2 Deposited 2015-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain O 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0
Resolution 3.50 Å R-free 0.253
5C3I Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2 Deposited 2015-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain S 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0
Resolution 3.50 Å R-free 0.253
5C3I Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2 Deposited 2015-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain W 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0
Resolution 3.50 Å R-free 0.253
5CPI Nucleosome containing unmethylated Sat2R DNA Deposited 2015-07-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.90 Å R-free 0.295
5CPJ Nucleosome containing methylated Sat2R DNA Deposited 2015-07-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 3.15 Å R-free 0.295
5CPK Nucleosome containing methylated Sat2L DNA Deposited 2015-07-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.63 Å R-free 0.284
5FA5 Crystal Structure of PRMT5:MEP50 in complex with MTA and H4 peptide Deposited 2015-12-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain C 2–21（20 aa） Fragment：DNA binding residues 2-21
Not recorded MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；281 K；200 mM ammonium sulfate, 20-28% PEG 3350, 2 mM 5-deoxy-5-(methylthio)adenosine, 1 mM H4 peptide (1-20)
Resolution 2.34 Å R-free 0.221
5FA5 Crystal Structure of PRMT5:MEP50 in complex with MTA and H4 peptide Deposited 2015-12-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 2–21（20 aa） Fragment：DNA binding residues 2-21
Not recorded MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；281 K；200 mM ammonium sulfate, 20-28% PEG 3350, 2 mM 5-deoxy-5-(methylthio)adenosine, 1 mM H4 peptide (1-20)
Resolution 2.34 Å R-free 0.221
5FA5 Crystal Structure of PRMT5:MEP50 in complex with MTA and H4 peptide Deposited 2015-12-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 2–21（20 aa） Fragment：DNA binding residues 2-21
Not recorded MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；281 K；200 mM ammonium sulfate, 20-28% PEG 3350, 2 mM 5-deoxy-5-(methylthio)adenosine, 1 mM H4 peptide (1-20)
Resolution 2.34 Å R-free 0.221
5FA5 Crystal Structure of PRMT5:MEP50 in complex with MTA and H4 peptide Deposited 2015-12-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 2–21（20 aa） Fragment：DNA binding residues 2-21
Not recorded MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；281 K；200 mM ammonium sulfate, 20-28% PEG 3350, 2 mM 5-deoxy-5-(methylthio)adenosine, 1 mM H4 peptide (1-20)
Resolution 2.34 Å R-free 0.221
5FWE JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H4(1-15)R3me2s PEPTIDE Deposited 2016-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–16（15 aa） Fragment：HISTONE H4(1-15)R3ME2S PEPTIDE, UNP RESIDUES 2-16
Non-standard monomer：Yes (specific site not provided by mmCIF) NI NICKEL (II) ION × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 OGA N-OXALYLGLYCINE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；SITTING DROPS, 277 K, 0.15 M POTASSIUM BROMIDE, 30 % W/V PEG 2000 MME, pH 7.5
Resolution 2.05 Å R-free 0.255
5FWE JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H4(1-15)R3me2s PEPTIDE Deposited 2016-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–16（15 aa） Fragment：HISTONE H4(1-15)R3ME2S PEPTIDE, UNP RESIDUES 2-16
Non-standard monomer：Yes (specific site not provided by mmCIF) NI NICKEL (II) ION × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 OGA N-OXALYLGLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；SITTING DROPS, 277 K, 0.15 M POTASSIUM BROMIDE, 30 % W/V PEG 2000 MME, pH 7.5
Resolution 2.05 Å R-free 0.255
5GSE Crystal structure of unusual nucleosome Deposited 2016-08-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；potassium bromide, potassium thiocyanate, Tris-HCl, PGA-LM, PEG 400
Resolution 3.14 Å R-free 0.255
5GSU Crystal structure of nucleosome core particle consisting of human testis-specific histone variants, Th2A and Th2B Deposited 2016-08-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded CL CHLORIDE ION × 3 MN MANGANESE (II) ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；20mM Pottasium Cacodylate pH 6.0, 60-70mM KCl, 70-90mM MnCl2
Resolution 3.10 Å R-free 0.257
5GT0 Crystal structure of nucleosome complex with human testis-specific histone variants, Th2a Deposited 2016-08-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded MN MANGANESE (II) ION × 14 CL CHLORIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；60-70mM KCl, 70-90mM MnCl2, 24% MPD
Resolution 2.82 Å R-free 0.280
5GT3 Crystal structure of nucleosome particle in the presence of human testis-specific histone variant, hTh2b Deposited 2016-08-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded MN MANGANESE (II) ION × 12 CL CHLORIDE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；60-70mM KCl, 70-90mM MnCl2, 24% MPD
Resolution 2.91 Å R-free 0.258
5GTC Crystal structure of complex between DMAP-SH conjugated with a Kaposi's sarcoma herpesvirus LANA peptide (5-15) and nucleosome core particle Deposited 2016-08-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.70 Å R-free 0.267
5GXQ The crystal structure of the nucleosome containing H3.6 Deposited 2016-09-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.85 Å R-free 0.262
5JA4 Crystal structure of human TONSL and MCM2 HBDs binding to a histone H3-H4 tetramer Deposited 2016-04-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 2–103（102 aa）
Not recorded MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；298 K；0.1M MES pH 5.6, 7% isopropanol
Resolution 2.42 Å R-free 0.246
5JRG Crystal structure of the nucleosome containing the DNA with tetrahydrofuran (THF) Deposited 2016-05-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.50 Å R-free 0.245
5KDM Crystal structure of EBV tegument protein BNRF1 in complex with histone chaperone DAXX and histones H3.3-H4 Deposited 2016-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 2–103（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；0.1M MES pH 6.0, 0.8 M ammonium sulfate
Resolution 3.50 Å R-free 0.280
5X7X The crystal structure of the nucleosome containing H3.3 at 2.18 angstrom resolution Deposited 2017-02-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.18 Å R-free 0.256
5XF3 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,R-configuration) Deposited 2017-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MG MAGNESIUM ION × 1 RUD [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 × 2 RRK (1R,2R)-1,2-diphenylethane-1,2-diamine × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；35-55 mM MnCl2, 25-49 mM KCl, 20 mM K-Cacodylate pH 6.0
Resolution 2.60 Å R-free 0.270
5XF4 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (S,S-configuration) Deposited 2017-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MG MAGNESIUM ION × 1 RUD [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 × 2 SSK (1S,2S)-1,2-diphenylethane-1,2-diamine × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；35-55 mM MnCl2, 25-49 mM KCl, 20 mM K-Cacodylate pH 6.0
Resolution 2.87 Å R-free 0.266
5XF5 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,S-configuration) Deposited 2017-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MG MAGNESIUM ION × 1 RUD [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 × 2 RSK (1S,2R)-1,2-diphenylethane-1,2-diamine × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；35-55mM MnCl2, 25-49mM KCl, 20mM K-Cacodylate pH 6.0
Resolution 2.82 Å R-free 0.264
5Y0C Crystal Structure of the human nucleosome at 2.09 angstrom resolution Deposited 2017-07-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 10 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.09 Å R-free 0.249
5Y0D Crystal Structure of the human nucleosome containing the H2B E76K mutant Deposited 2017-07-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 1.99 Å R-free 0.252
5Z23 Crystal structure of the nucleosome containing a chimeric histone H3/CENP-A CATD Deposited 2017-12-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.73 Å R-free 0.261
5Z30 The crystal structure of the nucleosome containing a cancer-associated histone H2A.Z R80C mutant Deposited 2018-01-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.45 Å R-free 0.243
5ZBX The crystal structure of the nucleosome containing histone H3.1 CATD(V76Q, K77D) Deposited 2018-02-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.58 Å R-free 0.249
6A5L RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA Deposited 2018-06-24 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.60 Å
6A5O RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome Deposited 2018-06-25 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.90 Å
6A5P RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome Deposited 2018-06-25 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å
6A5R RNA polymerase II elongation complex stalled at SHL(-2) of the nucleosome Deposited 2018-06-25 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
6A5T RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome Deposited 2018-06-25 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.70 Å
6A5U RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation Deposited 2018-06-25 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
6BUZ Cryo-EM structure of CENP-A nucleosome in complex with kinetochore protein CENP-N Deposited 2017-12-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.92 Å
6C0W Cryo-EM structure of human kinetochore protein CENP-N with the centromeric nucleosome containing CENP-A Deposited 2018-01-02 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–102（102 aa）
Chain F 1–102（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6E0C Cryo-EM structure of the CENP-A nucleosome (W601) in complex with a single chain antibody fragment Deposited 2018-07-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.63 Å
6E0P Cryo-EM structure of the centromeric nucleosome (Native alpha satellite DNA) in complex with a single chain antibody fragment Deposited 2018-07-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；blot for 2.5 sec before plunging
Resolution 2.60 Å
6FML CryoEM Structure INO80core Nucleosome complex Deposited 2018-01-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain N 2–103（102 aa）
Chain R 2–103（102 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM HEPES pH 8, 60 mM KCl, 0.5% glycerol, 0.25 mM CaCl2, 20 uM ZnCl2, 0.25 mM DTT, 0.05% Octyl-beta-glucoside
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.34 Å
6HKT Structure of an H1-bound 6-nucleosome array Deposited 2018-09-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 48 PDB declaration: 50-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Chain V 1–103（103 aa）
Chain Z 1–103（103 aa）
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Chain l 1–103（103 aa）
Chain p 1–103（103 aa）
Chain v 1–103（103 aa）
Chain z 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；293.15 K；15% MPD, 0.1 M NaCl and 0.1 M Tris pH 8.8
Resolution 9.70 Å R-free 0.286
6HTS Cryo-EM structure of the human INO80 complex bound to nucleosome Deposited 2018-10-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain J 1–103（103 aa）
Chain N 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
6INQ RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position) Deposited 2018-10-26 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
6IPU Human nucleosome core particle containing 145 bp of DNA Deposited 2018-11-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 22–103（82 aa）
Chain F 17–103（87 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；manganese chloride, potassium chloride, potassium cacodylate
Resolution 1.99 Å R-free 0.263
6IQ4 Nucleosome core particle cross-linked with a hetero-binuclear molecule possessing RAPTA and gold(I) 4-(diphenylphosphino)benzoic acid groups. Deposited 2018-11-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 22–103（82 aa）
Chain F 17–103（87 aa）
Not recorded AU GOLD ION × 1 XIS 4-diphenylphosphanylbenzoic acid × 1 MG MAGNESIUM ION × 4 D0X [Ru(eta(6)-p-cymene)Cl-2(pta) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；manganese chloride, potassium chloride, potassium cacodylate
Resolution 2.25 Å R-free 0.257
6IR9 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome Deposited 2018-11-12 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6J4W RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-5) of the nucleosome Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.90 Å
6J4X RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1A) Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Y RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1B) Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Z RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6J50 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome (tilted conformation) Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
6J51 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome, weak Elf1 (+1 position) Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6JOU Crystal structure of the human nucleosome containing H2A.Z.1 S42R Deposited 2019-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.17 Å R-free 0.250
6JR0 Crystal structure of the human nucleosome phased with 12 selenium atoms Deposited 2019-04-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.50 Å R-free 0.253
6JR1 Crystal structure of the human nucleosome phased with 16 selenium atoms Deposited 2019-04-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.40 Å R-free 0.243
6JXD Human nucleosome core particle with cohesive end DNA termini Deposited 2019-04-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 22–103（82 aa）
Chain F 17–103（87 aa）
Not recorded MN MANGANESE (II) ION × 17 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；manganese chloride, potassium chloride, potassium cacodylate
Resolution 2.25 Å R-free 0.292
6K1I Human nucleosome core particle with gammaH2A.X variant Deposited 2019-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 23 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；potassium chloride, manganese chloride, potassium cacodylate
Resolution 2.75 Å R-free 0.277
6K1J Human nucleosome core particle with H2A.X variant Deposited 2019-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；Potassium Chloride, Manganese Chloride, Potassium Cacodylate
Resolution 2.85 Å R-free 0.319
6K1K Human nucleosome core particle with H2A.X S139E variant Deposited 2019-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 33 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；potassium chloride, manganese chloride, potassium cacodylate
Resolution 2.20 Å R-free 0.275
6KE9 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-07-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 17–103（87 aa）
Chain F 17–103（87 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
Resolution 2.22 Å R-free 0.230
6KVD Crystal structure of human nucleosome containing H2A.J Deposited 2019-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 13 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.21 Å R-free 0.257
6KXV Crystal structure of a nucleosome containing Leishmania histone H3 Deposited 2019-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；sodium acetate, isopropanol, manganese chloride, trimethylamine N-oxide
Resolution 3.63 Å R-free 0.264
6L49 H3-CA-H3 tri-nucleosome with the 22 base-pair linker DNA Deposited 2019-10-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Chain T 1–103（103 aa）
Chain X 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 18.90 Å
6L4A H3-H3-H3 tri-nucleosome with the 22 base-pair linker DNA Deposited 2019-10-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Chain T 1–103（103 aa）
Chain X 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 12.30 Å
6L9H The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-11-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 17–103（87 aa）
Chain F 17–103（87 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
Resolution 2.60 Å R-free 0.278
6L9Z 338 bp di-nucleosome assembled with linker histone H1.X Deposited 2019-11-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded CL CHLORIDE ION × 8 CA CALCIUM ION × 65 K POTASSIUM ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；Calcium chloride, Potassium chloride, Potassium Cacodylate
Resolution 2.50 Å R-free 0.256
6LA2 343 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 Deposited 2019-11-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 34 PDB declaration: 38-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Chain V 1–103（103 aa）
Chain Z 1–103（103 aa）
Chain f 1–103（103 aa）
Chain j 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, Potassium chloride, Sodium acetate
Resolution 3.89 Å R-free 0.267
6LA8 349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 Deposited 2019-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded CA CALCIUM ION × 23 K POTASSIUM ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate (cryo-25% MPD)
Resolution 3.40 Å R-free 0.265
6LA9 349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 (high cryoprotectant) Deposited 2019-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded CA CALCIUM ION × 40 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
Resolution 3.70 Å R-free 0.266
6LAB 169 bp nucleosome, harboring cohesive DNA termini, assembled with linker histone H1.0 Deposited 2019-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded CA CALCIUM ION × 20 K POTASSIUM ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
Resolution 3.20 Å R-free 0.262
6LE9 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-11-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 17–103（87 aa）
Chain F 17–103（87 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
Resolution 2.60 Å R-free 0.281
6LER 169 bp nucleosome harboring non-identical cohesive DNA termini. Deposited 2019-11-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CA CALCIUM ION × 6 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
Resolution 3.00 Å R-free 0.261
6LER 169 bp nucleosome harboring non-identical cohesive DNA termini. Deposited 2019-11-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded CA CALCIUM ION × 8 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
Resolution 3.00 Å R-free 0.261
6M3V 355 bp di-nucleosome harboring cohesive DNA termini Deposited 2020-03-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded K POTASSIUM ION × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；291 K；Calcium chloride, Potassium chloride, Potassium Cacodylate, Poly glutamic acid
Resolution 4.60 Å R-free 0.261
6M44 355 bp di-nucleosome harboring cohesive DNA termini (high cryoprotectant) Deposited 2020-03-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；Calcium chloride, Potassium chloride, Potassium Cacodylate, Poly glutamic acid
Resolution 3.81 Å R-free 0.286
6M4D Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2 Deposited 2020-03-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
6M4G Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2 Deposited 2020-03-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6M4H Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2 Deposited 2020-03-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6MLC PHD6 domain of MLL3 in complex with histone H4 Deposited 2018-09-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain E 2–21（20 aa） Fragment：residues 2-21
Not recorded ZN ZINC ION × 42 GOL GLYCEROL × 6 UNX UNKNOWN LIGAND × 30 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；2 M Na-Form, 0.1 M Tris, pH 8.5
Resolution 1.80 Å R-free 0.216
6MLC PHD6 domain of MLL3 in complex with histone H4 Deposited 2018-09-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain F 2–21（20 aa） Fragment：residues 2-21
Not recorded ZN ZINC ION × 42 GOL GLYCEROL × 24 UNX UNKNOWN LIGAND × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；2 M Na-Form, 0.1 M Tris, pH 8.5
Resolution 1.80 Å R-free 0.216
6MUO CENP-A nucleosome bound by two copies of CENP-C(CD) and one copy CENP-N(NT) Deposited 2018-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 9–102（94 aa）
Chain F 9–102（94 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；10 mM HEPES, 50 mN NaCl, 1 mM EDTA, 1mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 8 seconds before plunging
Resolution 3.60 Å
6MUP CENP-A nucleosome bound by two copies of CENP-C(CD) and two copies CENP-N(NT) Deposited 2018-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 9–102（94 aa）
Chain F 9–102（94 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；10 mM HEPES, 50 mN NaCl, 1 mM EDTA, 1mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 8 seconds before plunging
Resolution 3.50 Å
6O1D Cryo-EM structure of the centromeric nucleosome with native alpha satellite DNA Deposited 2019-02-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；blot for 2.5 sec before plunging
Resolution 3.40 Å
6R0C Human-D02 Nucleosome Core Particle with biotin-streptavidin label Deposited 2019-03-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6R8Y Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB Deposited 2019-04-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6R8Z Cryo-EM structure of NCP_THF2(-1)-UV-DDB Deposited 2019-04-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6R90 Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A Deposited 2019-04-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6R91 Cryo-EM structure of NCP_THF2(-3)-UV-DDB Deposited 2019-04-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6R92 Cryo-EM structure of NCP-THF2(+1)-UV-DDB class B Deposited 2019-04-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
6R93 Cryo-EM structure of NCP-6-4PP Deposited 2019-04-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6R94 Cryo-EM structure of NCP_THF2(-3) Deposited 2019-04-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6RNY PFV intasome - nucleosome strand transfer complex Deposited 2019-05-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: octadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE；1 min incubation 3.5s blot
Resolution 3.90 Å
6RXS Crystal structure of CobB Ac3(A76G,Y92A, I131L, V187Y) in complex with H4K16-Acetyl peptide Deposited 2019-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 13–23（11 aa） Fragment：H4K16Ac
Mutation：K16ALY Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.1M Bis-Tris, 0.03 M HCl, 23% PEG3350
Resolution 1.60 Å R-free 0.205
6SE0 Class 1 : CENP-A nucleosome Deposited 2019-07-29 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6SE6 Class2 : CENP-A nucleosome in complex with CENP-C central region Deposited 2019-07-29 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6SEE Class2A : CENP-A nucleosome in complex with CENP-C central region Deposited 2019-07-29 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6SEF Class2C : CENP-A nucleosome in complex with CENP-C central region Deposited 2019-07-29 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6SEG Class1: CENP-A nucleosome in complex with CENP-C central region Deposited 2019-07-30 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6T79 Structure of a human nucleosome at 3.2 A resolution Deposited 2019-10-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 3.20 Å
6T7A Structure of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 3.70 Å
6T7B Structure of human Sox2 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 5.10 Å
6T7C Structure of two copies of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 4.00 Å
6T7D Structure of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 4.40 Å
6T90 OCT4-SOX2-bound nucleosome - SHL-6 Deposited 2019-10-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded PTD PENTANEDIAL × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
6T93 Nucleosome with OCT4-SOX2 motif at SHL-6 Deposited 2019-10-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.49 Å
6UPK Structure of FACT_subnucleosome complex 1 Deposited 2019-10-17 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.90 Å
6UPL Structure of FACT_subnucleosome complex 2 Deposited 2019-10-17 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.40 Å
6USJ Structure of two nucleosomes bridged by human PARP2 Deposited 2019-10-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Buffer was pH-adjusted and filtered through a 0.22 um filter.
cryo-EM vitrification conditions Cryogen ETHANE；Blot time 2s, blot force 0
Resolution 10.50 Å
6V2K The nucleosome structure after H2A-H2B exchange Deposited 2019-11-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.60 Å R-free 0.248
6V92 RSC-NCP Deposited 2019-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 33 PDB declaration: 35-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 20.00 Å
6VO5 Crystal structure of Human histone acetytransferas 1 (HAT1) in complex with isobutryl-COA and K12A mutant variant of histone H4 Deposited 2020-01-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–21（20 aa）
Not recorded ACT ACETATE ION × 1 CO6 ISOBUTYRYL-COENZYME A × 1 GOL GLYCEROL × 1 SO4 SULFATE ION × 1 UNX UNKNOWN LIGAND × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；12% PEG 20K and 0.1M MES pH6.5
Resolution 1.60 Å R-free 0.198
6VO5 Crystal structure of Human histone acetytransferas 1 (HAT1) in complex with isobutryl-COA and K12A mutant variant of histone H4 Deposited 2020-01-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–21（20 aa）
Not recorded CO6 ISOBUTYRYL-COENZYME A × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 1 UNX UNKNOWN LIGAND × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；12% PEG 20K and 0.1M MES pH6.5
Resolution 1.60 Å R-free 0.198
6X59 The mouse cGAS catalytic domain binding to human assembled nucleosome Deposited 2020-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
6X5A The mouse cGAS catalytic domain binding to human nucleosome that purified from HEK293T cells Deposited 2020-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.36 Å
6XJD Two mouse cGAS catalytic domain binding to human assembled nucleosome Deposited 2020-06-23 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.80 Å
6Y5D Structure of human cGAS (K394E) bound to the nucleosome Deposited 2020-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain N 1–103（103 aa）
Chain R 1–103（103 aa）
Not recorded PTD PENTANEDIAL × 9 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6Y5E Structure of human cGAS (K394E) bound to the nucleosome (focused refinement of cGAS-NCP subcomplex) Deposited 2020-02-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 23–103（81 aa）
Chain F 21–103（83 aa）
Not recorded PTD PENTANEDIAL × 8 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
6YOV OCT4-SOX2-bound nucleosome - SHL+6 Deposited 2020-04-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded PTD PENTANEDIAL × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.42 Å
7A08 CryoEM Structure of cGAS Nucleosome complex Deposited 2020-08-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain e 2–103（102 aa）
Chain i 2–103（102 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.11 Å
7BWD Structure of Dot1L-H2BK34ub Nucleosome Complex Deposited 2020-04-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.32 Å
7BXT The cryo-EM structure of CENP-A nucleosome in complex with CENP-C peptide and CENP-N N-terminal domain Deposited 2020-04-20 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7BY0 The cryo-EM structure of CENP-A nucleosome in complex with the phosphorylated CENP-C Deposited 2020-04-21 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–102（102 aa）
Chain F 1–102（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7C0M Human cGAS-nucleosome complex Deposited 2020-05-01 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Chain b 2–103（102 aa）
Chain f 2–103（102 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7CIZ Crystal structure of DNAJC9 HBD helix2 in complex with H3.3-H4 dimer and MCM2 HBD Deposited 2020-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 2–103（102 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.05 M Lithium sulfate, 0.05 M Sodium sulfate; 0.05 M Tris, pH 8.5, 30% (v/v) PEG400.
Resolution 1.80 Å R-free 0.214
7CIZ Crystal structure of DNAJC9 HBD helix2 in complex with H3.3-H4 dimer and MCM2 HBD Deposited 2020-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.05 M Lithium sulfate, 0.05 M Sodium sulfate; 0.05 M Tris, pH 8.5, 30% (v/v) PEG400.
Resolution 1.80 Å R-free 0.214
7CIZ Crystal structure of DNAJC9 HBD helix2 in complex with H3.3-H4 dimer and MCM2 HBD Deposited 2020-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain J 2–103（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.05 M Lithium sulfate, 0.05 M Sodium sulfate; 0.05 M Tris, pH 8.5, 30% (v/v) PEG400.
Resolution 1.80 Å R-free 0.214
7CJ0 Crystal structure of DNAJC9 HBD in complex with H3.3-H4 dimer and MCM2 HBD Deposited 2020-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 2–103（102 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.17 M Sodium acetate, 0.1 M Tris, pH8.5, 25% (v/v) PEG 4000, 20% (v/v) Glycerol
Resolution 2.50 Å R-free 0.295
7CJ0 Crystal structure of DNAJC9 HBD in complex with H3.3-H4 dimer and MCM2 HBD Deposited 2020-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 2–103（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.17 M Sodium acetate, 0.1 M Tris, pH8.5, 25% (v/v) PEG 4000, 20% (v/v) Glycerol
Resolution 2.50 Å R-free 0.295
7COW 353 bp di-nucleosome harboring cohesive DNA termini with linker histone H1.0 Deposited 2020-08-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded CA CALCIUM ION × 3 K POTASSIUM ION × 5 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；potassium acetate, calcium chloride, potassium chloride
Resolution 2.86 Å R-free 0.297
7D1Z Cryo-EM structure of SET8-nucleosome complex Deposited 2020-09-15 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
7D20 Cryo-EM structure of SET8-CENP-A-nucleosome complex Deposited 2020-09-15 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7DBP Linker histone defines structure and self-association behaviour of the 177 bp human chromosome Deposited 2020-10-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7E8D NSD2 E1099K mutant bound to nucleosome Deposited 2021-03-01 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ZN ZINC ION × 3 SFG SINEFUNGIN × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7EIC Crystal structure of AF9 YEATS domain in complex with H4K5acK8ac peptide Deposited 2021-03-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–13（12 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 2 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Bis-Tris buffer (pH 6.5) containing 100 mM ammonium acetate and 25% PEG3350
Resolution 1.95 Å R-free 0.205
7JO9 1:1 cGAS-nucleosome complex Deposited 2020-08-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7JOA 2:1 cGAS-nucleosome complex Deposited 2020-08-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7JZV Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome Deposited 2020-09-02 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain Q 2–103（102 aa）
Chain q 2–103（102 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7K5X Cryo-EM structure of a chromatosome containing human linker histone H1.0 Deposited 2020-09-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.93 Å
7K5Y Cryo-EM structure of a chromatosome containing human linker histone H1.4 Deposited 2020-09-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
7K60 Cryo-EM structure of a chromatosome containing human linker histone H1.10 Deposited 2020-09-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
7K61 Cryo-EM structure of 197bp nucleosome aided by scFv Deposited 2020-09-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.85 Å
7K63 Cryo-EM structure of a chromatosome containing chimeric linker histone gH1.10-ncH1.4 Deposited 2020-09-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
7LMK Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me3 Deposited 2021-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 15–27（13 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；13% PEG1500, 20 mM DTT and 200 mM L-proline, 0.1 M HEPES (pH 7.5)
Resolution 2.65 Å R-free 0.258
7LMK Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me3 Deposited 2021-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 15–27（13 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；13% PEG1500, 20 mM DTT and 200 mM L-proline, 0.1 M HEPES (pH 7.5)
Resolution 2.65 Å R-free 0.258
7LMK Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me3 Deposited 2021-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 15–27（13 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；13% PEG1500, 20 mM DTT and 200 mM L-proline, 0.1 M HEPES (pH 7.5)
Resolution 2.65 Å R-free 0.258
7LMK Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me3 Deposited 2021-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain I 15–27（13 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；13% PEG1500, 20 mM DTT and 200 mM L-proline, 0.1 M HEPES (pH 7.5)
Resolution 2.65 Å R-free 0.258
7LMM Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me2 Deposited 2021-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 15–27（13 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1 M MES (pH 6.5) ,13% PEG1500, 20 mM DTT and 200 mM L-proline
Resolution 2.80 Å R-free 0.267
7LMM Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me2 Deposited 2021-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 15–27（13 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1 M MES (pH 6.5) ,13% PEG1500, 20 mM DTT and 200 mM L-proline
Resolution 2.80 Å R-free 0.267
7LMM Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me2 Deposited 2021-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain I 15–27（13 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1 M MES (pH 6.5) ,13% PEG1500, 20 mM DTT and 200 mM L-proline
Resolution 2.80 Å R-free 0.267
7LMM Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me2 Deposited 2021-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 15–27（13 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1 M MES (pH 6.5) ,13% PEG1500, 20 mM DTT and 200 mM L-proline
Resolution 2.80 Å R-free 0.267
7LYA Cryo-EM structure of the human nucleosome core particle with linked histone proteins H2A and H2B Deposited 2021-03-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.91 Å
7LYB Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c Deposited 2021-03-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.28 Å
7LYC Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A Lys13 and Lys15 in complex with BARD1 (residues 415-777) Deposited 2021-03-06 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
7M98 ATAD2 bromodomain complexed with histone H4K5ac (res 1-10) ligand Deposited 2021-03-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–16（15 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；2.0 M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, pH 6.6
Resolution 1.60 Å R-free 0.219
7NL0 Cryo-EM structure of the Lin28B nucleosome core particle Deposited 2021-02-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7PET The 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 34 PDB declaration: 36-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Chain l 1–103（103 aa）
Chain p 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.50 Å
7PEU Trinucleosome of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
7PEV Nucleosome stack of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.00 Å
7PEW Nucleosome 1 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
7PEX Nucleosome 2 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
7PEY Nucleosome 3 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7PEZ Nucleosome 4 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain l 1–103（103 aa）
Chain p 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.90 Å
7PF0 Trinucleosome of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.00 Å
7PF2 Nucleosome stack of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
7PF3 Nucleosome 4 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain l 1–103（103 aa）
Chain p 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7PF4 Nucleosome 3 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7PF5 Nucleosome 2 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7PF6 Nucleosome 1 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7PFA Trinucleosome of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.70 Å
7PFC Nucleosome stack of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
7PFD Nucleosome 1 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7PFE Nucleosome 2 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7PFF Nucleosome 3 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7PFT Trinucleosome of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.80 Å
7PFU Nucleosome stack of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.00 Å
7PFV Nucleosome 1 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7PFW Nucleosome 2 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.20 Å
7PFX Nucleosome 3 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7PII Structure of the human CCAN CENP-A alpha-satellite complex Deposited 2021-08-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.68 Å
7R5R Structure of the human CCAN CENP-A alpha-satellite complex Deposited 2022-02-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.44 Å
7SCY Nuc147 bound to single BRCT Deposited 2021-09-29 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7SCZ Nuc147 bound to multiple BRCTs Deposited 2021-09-29 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7TAN Structure of VRK1 C-terminal tail bound to nucleosome core particle Deposited 2021-12-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.00 Å
7U0G structure of LIN28b nucleosome bound 3 OCT4 Deposited 2022-02-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
7U0I Structure of LIN28b nucleosome bound 2 OCT4 Deposited 2022-02-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
7U0J Structure of 162bp LIN28b nucleosome Deposited 2022-02-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7U46 Cryo-EM structure of CENP-A nucleosome (palindromic alpha satellite DNA) in complex with CENP-N Deposited 2022-02-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.68 Å
7U47 CryoEM structure of CENP-N promoted nucleosome stacks with CENP-A and palindromic alpha satellite DNA sequence Deposited 2022-02-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain M 1–103（103 aa）
Chain Q 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.50 Å
7U4D CryoEM structure of CENP-N promoted nucleosome stacks with CENP-A and 601 DNA sequence Deposited 2022-02-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain M 1–103（103 aa）
Chain Q 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.10 Å
7U50 APE1 bound to a nucleosome core particle with AP-site at SHL-6 Deposited 2022-03-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7U51 Nucleosome core particle with AP-site at SHL-6 Deposited 2022-03-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7U52 nucleosome core particle with AP-site at SHL-6.5 Deposited 2022-03-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7U53 Nucleosome core particle with AP-site at SHL0 Deposited 2022-03-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7UV9 KDM2A-nucleosome structure stabilized by H3K36C-UNC8015 covalent conjugate Deposited 2022-04-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded OH0 N-heptanoyl-N-hydroxy-beta-alanine × 1 FE FE (III) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.20 Å
7V1M Structural basis for the co-chaperone relationship of sNASP and ASF1b Deposited 2021-08-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 2–103（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；8% v/v Tacsimate, pH 6.0, 20% w/v PEG 3350
Resolution 2.83 Å R-free 0.240
7V1M Structural basis for the co-chaperone relationship of sNASP and ASF1b Deposited 2021-08-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 2–103（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；8% v/v Tacsimate, pH 6.0, 20% w/v PEG 3350
Resolution 2.83 Å R-free 0.240
7V6Q Crystal structure of sNASP-ASF1A-H3.1-H4 complex Deposited 2021-08-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 3–103（101 aa）
Not recorded GOL GLYCEROL × 4 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；18% (v/v) Tacsimate, pH 5.0 11% (v/v) PEG2000MME
Resolution 3.00 Å R-free 0.203
7V6Q Crystal structure of sNASP-ASF1A-H3.1-H4 complex Deposited 2021-08-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain G 3–103（101 aa）
Not recorded GOL GLYCEROL × 2 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；18% (v/v) Tacsimate, pH 5.0 11% (v/v) PEG2000MME
Resolution 3.00 Å R-free 0.203
7V90 Telomeric mononucleosome Deposited 2021-08-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7V96 Telomeric Dinucleosome Deposited 2021-08-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.92 Å
7V9C Telomeric Dinucleosome in open state Deposited 2021-08-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7V9J Telomeric trinucleosome Deposited 2021-08-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Chain T 1–103（103 aa）
Chain X 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.00 Å
7V9K Telomeric tetranucleosome Deposited 2021-08-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 34-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Chain T 1–103（103 aa）
Chain X 1–103（103 aa）
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.10 Å
7V9S Telomeric trinucleosome in open state Deposited 2021-08-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Chain T 1–103（103 aa）
Chain X 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.00 Å
7VA4 Telomeric tetranucleosome in open state Deposited 2021-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 34-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Chain T 1–103（103 aa）
Chain X 1–103（103 aa）
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 14.00 Å
7VCQ structure of viral protein BKRF4 in complex with H3.3-H4-ASF1 Deposited 2021-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2% Tacsimate pH 7.0; o.1M HEPES pH 7.5; 20% PEG3350
Resolution 3.00 Å R-free 0.283
7VCQ structure of viral protein BKRF4 in complex with H3.3-H4-ASF1 Deposited 2021-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2% Tacsimate pH 7.0; o.1M HEPES pH 7.5; 20% PEG3350
Resolution 3.00 Å R-free 0.283
7VCQ structure of viral protein BKRF4 in complex with H3.3-H4-ASF1 Deposited 2021-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2% Tacsimate pH 7.0; o.1M HEPES pH 7.5; 20% PEG3350
Resolution 3.00 Å R-free 0.283
7VZ4 Cryo-EM structure of human nucleosome core particle composed of the Widom 601L DNA sequence Deposited 2021-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 1.89 Å
7W9V Cryo-EM structure of nucleosome in complex with p300 acetyltransferase catalytic core (complex I) Deposited 2021-12-10 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.95 Å
7WBV RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome Deposited 2021-12-17 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain b 2–103（102 aa）
Chain f 2–103（102 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7WBW RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3.5) of the nucleosome Deposited 2021-12-17 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain b 2–103（102 aa）
Chain f 2–103（102 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.10 Å
7WBX RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome Deposited 2021-12-17 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain b 2–103（102 aa）
Chain f 2–103（102 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7X57 Cryo-EM structure of human subnucleosome (closed form) Deposited 2022-03-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain D 1–103（103 aa）
Chain F 1–103（103 aa）
Chain H 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.63 Å
7X58 Cryo-EM structure of human subnucleosome (open form) Deposited 2022-03-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain D 2–103（102 aa）
Chain F 2–103（102 aa）
Chain H 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.93 Å
7XSE RNA polymerase II elongation complex transcribing a nucleosome (EC42) Deposited 2022-05-13 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7XSX RNA polymerase II elongation complex transcribing a nucleosome (EC49) Deposited 2022-05-15 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7XSZ RNA polymerase II elongation complex transcribing a nucleosome (EC115) Deposited 2022-05-15 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7XT7 RNA polymerase II elongation complex transcribing a nucleosome (EC49B) Deposited 2022-05-16 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7XTD RNA polymerase II elongation complex transcribing a nucleosome (EC58oct) Deposited 2022-05-16 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7XTI RNA polymerase II elongation complex transcribing a nucleosome (EC58hex) Deposited 2022-05-17 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7XVL Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an DNA fragment) Deposited 2022-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain V 1–103（103 aa）
Chain Z 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 3.51 Å R-free 0.280
7XVL Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an DNA fragment) Deposited 2022-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Chain f 1–103（103 aa）
Chain j 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 3.51 Å R-free 0.280
7XVM Crystal Structure of Nucleosome-H5 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded CA CALCIUM ION × 18 CL CHLORIDE ION × 3 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 2.84 Å R-free 0.259
7XX5 Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded CA CALCIUM ION × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 3.19 Å R-free 0.259
7XX6 Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded CA CALCIUM ION × 21 K POTASSIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 3.39 Å R-free 0.296
7XX6 Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric
Chain V 1–103（103 aa）
Chain Z 1–103（103 aa）
Chain f 1–103（103 aa）
Chain j 1–103（103 aa）
Not recorded CA CALCIUM ION × 26 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 3.39 Å R-free 0.296
7XZX Cryo-EM structure of the nucleosome in complex with p53 DNA-binding domain Deposited 2022-06-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.53 Å
7XZY Cryo-EM structure of the nucleosome containing 193 base-pair DNA with a p53 target sequence Deposited 2022-06-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.97 Å
7XZZ Cryo-EM structure of the nucleosome in complex with p53 Deposited 2022-06-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.07 Å
7Y00 Cryo-EM structure of the nucleosome containing 169 base-pair DNA with a p53 target sequence Deposited 2022-06-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.96 Å
7Y5U Cryo-EM structure of the monomeric human CAF1LC-H3-H4 complex Deposited 2022-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7Y5V Cryo-EM structure of the dimeric human CAF1LC-H3-H4 complex Deposited 2022-06-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain E 1–103（103 aa）
Chain J 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.10 Å
7Y5W Cryo-EM structure of the left-handed Di-tetrasome Deposited 2022-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain D 1–103（103 aa）
Chain F 1–103（103 aa）
Chain H 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7Y60 Cryo-EM structure of human CAF1LC bound right-handed Di-tetrasome Deposited 2022-06-18 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain D 1–103（103 aa）
Chain F 1–103（103 aa）
Chain H 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7Y61 Cryo-EM structure of the two CAF1LCs bound right-handed Di-tetrasome Deposited 2022-06-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–103（103 aa）
Chain D 1–103（103 aa）
Chain F 1–103（103 aa）
Chain H 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.60 Å
7Y7I chicken KNL2 in complex with the CENP-A nucleosome Deposited 2022-06-22 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.42 Å
7YOZ Cryo-EM structure of human subnucleosome (intermediate form) Deposited 2022-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain D 1–103（103 aa）
Chain F 1–103（103 aa）
Chain H 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7YWX Structure of the human CCAN CENP-A alpha-satellite complex Deposited 2022-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 12.00 Å
7YYH Structure of the human CCANdeltaT CENP-A alpha-satellite complex Deposited 2022-02-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.90 Å
7ZI4 Cryo-EM structure of the human INO80 complex bound to a WT nucleosome Deposited 2022-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain J 1–103（103 aa）
Chain N 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；4uL of sample applied to Quantifoil R2/2 Cu 300 mesh grids. blot parameters were wait time 30 sec, blot time 0.5 sec, blot force -8
Resolution 3.20 Å
8AAG H1-bound palindromic nucleosome, state 1 Deposited 2022-07-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 10.00 Å
8ATF Nucleosome-bound Ino80 ATPase Deposited 2022-08-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain N 2–103（102 aa）
Chain R 2–103（102 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.45 Å
8AV6 CryoEM structure of INO80 core nucleosome complex in closed grappler conformation Deposited 2022-08-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain N 2–103（102 aa）
Chain R 2–103（102 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.68 Å
8DK5 Structure of 187bp LIN28b nucleosome with site 0 mutation Deposited 2022-07-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.71 Å
8EVG 162bp CX3CR1 nucleosome (further classified with better nucleosome end) Deposited 2022-10-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.75 Å
8EVH CX3CR1 nucleosome and wild type PU.1 complex Deposited 2022-10-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.85 Å
8EVI CX3CR1 nucleosome and PU.1 complex containing disulfide bond mutations Deposited 2022-10-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.64 Å
8EVJ CX3CR1 nucleosome bound PU.1 and C/EBPa Deposited 2022-10-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8GUI Bre1-nucleosome complex (Model I) Deposited 2022-09-12 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.81 Å
8GUJ Bre1-nucleosome complex (Model II) Deposited 2022-09-12 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8GUK Human nucleosome core particle (free form) Deposited 2022-09-12 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.51 Å
8H0V RNA polymerase II transcribing a chromatosome (type I) Deposited 2022-09-30 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8H0W RNA polymerase II transcribing a chromatosome (type II) Deposited 2022-09-30 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8H1T Cryo-EM structure of BAP1-ASXL1 bound to chromatosome Deposited 2022-10-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8HE5 RNA polymerase II elongation complex bound with Rad26 and Elf1, stalled at SHL(-3.5) of the nucleosome Deposited 2022-11-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 25-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.95 Å
8HLW Crystal structure of SIRT3 in complex with H4K16la peptide Deposited 2022-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 14–21（8 aa） Fragment：residues 20-27, with lactylated No.23 lysine
Not recorded ZN ZINC ION × 1 2OP (2S)-2-HYDROXYPROPANOIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；0.1 M Tris pH 8.5, 25% (w/v) Polyethylene glycol 3350
Resolution 2.50 Å R-free 0.243
8IEG Bre1(mRBD-RING)/Rad6-Ub/nucleosome complex Deposited 2023-02-15 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain F 23–102（80 aa）
Chain L 23–102（80 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.44 Å
8IEJ RNF20-RNF40/hRad6A-Ub/nucleosome complex Deposited 2023-02-15 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain F 23–102（80 aa）
Chain L 23–102（80 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
8IHL Overlapping tri-nucleosome Deposited 2023-02-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain N 1–103（103 aa）
Chain R 1–103（103 aa）
Chain V 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.64 Å
8IQF Cryo-EM structure of the dimeric human CAF1-H3-H4 complex Deposited 2023-03-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain E 1–103（103 aa）
Chain J 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8IQG Cryo-EM structure of the monomeric human CAF1-H3-H4 complex Deposited 2023-03-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8J6S Cryo-EM structure of the single CAF-1 bound right-handed Di-tetrasome Deposited 2023-04-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain D 1–103（103 aa）
Chain F 1–103（103 aa）
Chain H 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8J6T Cryo-EM structure of the double CAF-1 bound right-handed Di-tetrasome Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–103（103 aa）
Chain D 1–103（103 aa）
Chain F 1–103（103 aa）
Chain H 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.60 Å
8JBX Human canonical 601 DNA nucleosome Deposited 2023-05-09 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
8JCC Human histone H2B variant H2BFWT Cryo-EM structure with 601 DNA sequence Deposited 2023-05-10 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.42 Å
8JCD Human H2BFWTH100R nucleosome with 601 DNA Deposited 2023-05-11 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.14 Å
8JH2 RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.70 Å
8JH3 RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8JH4 RNA polymerase II elongation complex containing 60 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8JHF Native SUV420H1 bound to 167-bp nucleosome Deposited 2023-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 18–103（86 aa）
Chain F 18–103（86 aa）
Mutation：K20M Mutation：K20M ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane
Resolution 3.68 Å
8JHG Native SUV420H1 bound to 167-bp nucleosome Deposited 2023-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 18–103（86 aa）
Chain F 18–103（86 aa）
Mutation：K20M Mutation：K20M ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane
Resolution 3.58 Å
8JL9 Cryo-EM structure of the human nucleosome with scFv Deposited 2023-06-02 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.65 Å
8JLA Cryo-EM structure of the human nucleosome lacking N-terminal region of H2A, H2B, H3, and H4 Deposited 2023-06-02 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 17–103（87 aa）
Chain F 17–103（87 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.44 Å
8JLB Cryo-EM structure of the 145 bp human nucleosome containing H3.2 C110A mutant Deposited 2023-06-02 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.36 Å
8JLD Cryo-EM structure of the 145 bp human nucleosome containing acetylated H3 tail Deposited 2023-06-02 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.48 Å
8JND The cryo-EM structure of the nonameric RAD51 ring bound to the nucleosome with the linker DNA binding Deposited 2023-06-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 19-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.66 Å
8JNE The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome without the linker DNA binding Deposited 2023-06-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.68 Å
8JNF The cryo-EM structure of the RAD51 filament bound to the nucleosome Deposited 2023-06-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.91 Å
8KB5 Cryo-EM structure of the human nucleosome containing H3.8 Deposited 2023-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.26 Å
8KCY Structure of nucleosome complexed with two DEK molecules Deposited 2023-08-08 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8KD1 Structure of nucleosome complexed with one DEK molecule Deposited 2023-08-08 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8KE0 Structure of H1.2 bound to the nucleosome Deposited 2023-08-11 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8OFF Structure of BARD1 ARD-BRCTs in complex with H2AKc15ub nucleosomes (Map1) Deposited 2023-03-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain Da 1–103（103 aa）
Chain Db 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；blot force = 0 N blot time = 8 s
Resolution 3.40 Å
8OL1 cGAS-Nucleosome in complex with SPSB3-ELOBC (composite structure) Deposited 2023-03-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 23–103（81 aa）
Chain F 23–103（81 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；PBS buffer
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8OO7 CryoEM Structure INO80core Hexasome complex composite model state1 Deposited 2023-04-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain N 2–103（102 aa）
Chain R 2–103（102 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 7 ALF TETRAFLUOROALUMINATE ION × 1 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；30mM HEPES, pH7.5 50mM NaCl 0.25mM CaCl2 0.25mM DTT 2mM ADP 3.3mM MgCl2 10mM NaF 2mM AlCl3 0.05% octyl-beta-glucoside
cryo-EM vitrification conditions Cryogen ETHANE；wait time of 5s, blot force at 3, and a blot time of 2s with Whatman blotting paper (Cytiva, CAT No. 10311807)
Resolution 2.80 Å
8OOA CryoEM Structure INO80core Hexasome complex Hexasome refinement state1 Deposited 2023-04-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain N 2–103（102 aa）
Chain R 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；30mM HEPES, pH7.5 50mM NaCl 0.25mM CaCl2 0.25mM DTT 2mM ADP 3.3mM MgCl2 10mM NaF 2mM AlCl3 0.05% octyl-beta-glucoside
cryo-EM vitrification conditions Cryogen ETHANE；wait time of 5s, blot force at 3, and a blot time of 2s with Whatman blotting paper (Cytiva, CAT No. 10311807)
Resolution 3.18 Å
8OOP CryoEM Structure INO80core Hexasome complex composite model state2 Deposited 2023-04-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain N 2–103（102 aa）
Chain R 2–103（102 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 7 MG MAGNESIUM ION × 2 ALF TETRAFLUOROALUMINATE ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；30mM HEPES, pH7.5 50mM NaCl 0.25mM CaCl2 0.25mM DTT 2mM ADP 3.3mM MgCl2 10mM NaF 2mM AlCl3 0.05% octyl-beta-glucoside
cryo-EM vitrification conditions Cryogen ETHANE；wait time of 5s, blot force at 3, and a blot time of 2s with Whatman blotting paper (Cytiva, CAT No. 10311807)
Resolution 2.70 Å
8OOS CryoEM Structure INO80core Hexasome complex ATPase-hexasome refinement state 2 Deposited 2023-04-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain N 2–103（102 aa）
Chain R 2–103（102 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ALF TETRAFLUOROALUMINATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；30mM HEPES, pH7.5 50mM NaCl 0.25mM CaCl2 0.25mM DTT 2mM ADP 3.3mM MgCl2 10mM NaF 2mM AlCl3 0.05% octyl-beta-glucoside
cryo-EM vitrification conditions Cryogen ETHANE；wait time of 5s, blot force at 3, and a blot time of 2s with Whatman blotting paper (Cytiva, CAT No. 10311807)
Resolution 3.29 Å
8OSJ Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL-6.2 (DNA conformation 1) Deposited 2023-04-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
8OSK Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL+5.8 (composite map) Deposited 2023-04-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8OSL Cryo-EM structure of CLOCK-BMAL1 bound to the native Por enhancer nucleosome (map 2, additional 3D classification and flexible refinement) Deposited 2023-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.90 Å
8OTS OCT4 and MYC-MAX co-bound to a nucleosome Deposited 2023-04-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded PTD PENTANEDIAL × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8OTT MYC-MAX bound to a nucleosome at SHL+5.8 Deposited 2023-04-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 22–103（82 aa）
Chain F 22–103（82 aa）
Not recorded PTD PENTANEDIAL × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8OX0 Structure of apo telomeric nucleosome Deposited 2023-04-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；25 mM HEPES-KOH pH 8.0, 150 mM KCl, 1 mM MgCl2, 1% glycerol, 0.01% Igepal CA-630,1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；Blot Force: -15 Blot Time: 2.5 s
Resolution 2.52 Å
8OX1 Structure of TRF1core in complex with telomeric nucleosome Deposited 2023-04-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；25 mM HEPES-KOH pH 8.0, 150 mM KCl, 1 mM MgCl2, 1% glycerol, 0.01% Igepal CA-630, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；Blot Force: -15 Blot Time: 2.5 s
Resolution 2.70 Å
8PEF Crystal structure of SLF1 Ankyrin repeat domain in complex with H4 tail (K20me0) Deposited 2023-06-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 10–26（17 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.1M Sodium malonate dibasic monohydrate 0.1M Hepes pH 7 30% (w/v) Poly(acrylic acid sodium salt) 2100
Resolution 1.28 Å R-free 0.225
8Q36 Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Foamy Virus GAG Peptide-Au[I] Compound) Deposited 2023-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain BBB 17–103（87 aa）
Chain FFF 17–103（87 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0].
Resolution 2.60 Å R-free 0.262
8Q3E High Resolution Structure of Nucleosome Core with Bound Foamy Virus GAG Peptide Deposited 2023-08-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain BBB 17–103（87 aa）
Chain FFF 17–103（87 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
Resolution 2.17 Å R-free 0.270
8Q3M Structure of Nucleosome Core with a Bound Kaposi Sarcoma Associated Herpesvirus LANA Peptide Having a Methionine to Ornithine Substitution Deposited 2023-08-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain BBB 17–103（87 aa）
Chain FFF 17–103（87 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
Resolution 2.50 Å R-free 0.268
8Q3X Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Kaposi Sarcoma Associated Herpesvirus LANA Peptide-Au[I] Compound) Deposited 2023-08-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain BBB 17–103（87 aa）
Chain FFF 17–103（87 aa）
Not recorded AU GOLD ION × 1 XIS 4-diphenylphosphanylbenzoic acid × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
Resolution 2.30 Å R-free 0.262
8QZM Structure of DNMT3A1 UDR region bound to H2AK119ub nucleosome Deposited 2023-10-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5, 65 mM NaCl, 1 mM DTT, 0.1 mM S-Adenosyl methionine
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8RBX Structure of Integrator-PP2A bound to a paused RNA polymerase II-DSIF-NELF-nucleosome complex Deposited 2023-12-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 43 PDB declaration: 46-meric
Chain O 1–103（103 aa）
Chain U 1–103（103 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8RGM Cryo-EM structure of nucleosome containing Widom603 DNA Deposited 2023-12-14 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8SB6 Structure of human BRD2-BD1 bound to a histone H4 acetyl-methyllysine peptide Deposited 2023-04-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–16（15 aa） Fragment：N-terminal peptide (UNP residues 2-16)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M MES, pH 6.7, 20-25% PEG5000 MME, 0.2 M ammonium sulfate
Resolution 1.80 Å R-free 0.204
8SB6 Structure of human BRD2-BD1 bound to a histone H4 acetyl-methyllysine peptide Deposited 2023-04-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 2–16（15 aa） Fragment：N-terminal peptide (UNP residues 2-16)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M MES, pH 6.7, 20-25% PEG5000 MME, 0.2 M ammonium sulfate
Resolution 1.80 Å R-free 0.204
8SMW Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 1) Deposited 2023-04-26 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8SMX Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 2) Deposited 2023-04-26 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SMY Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 3) Deposited 2023-04-26 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SMZ Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (Class 4) Deposited 2023-04-26 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SN0 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 5) Deposited 2023-04-26 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SN1 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 6) Deposited 2023-04-26 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8SN2 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c (UbcH5c chemically conjugated to histone H2A) Deposited 2023-04-26 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8SN3 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8SN4 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN5 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 3) Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8SN6 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 4) Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN7 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 5) Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN8 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 6) Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN9 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8SNA Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8SPS High resolution structure of ESRRB nucleosome bound OCT4 at site a and site b Deposited 2023-05-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8SPU Structure of ESRRB nucleosome bound OCT4 at site c Deposited 2023-05-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8SYP Genomic CX3CR1 nucleosome Deposited 2023-05-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8TGP Crystal structure of SIRT2 with FAM-PEG4-H4K16(myristoyl) peptide Deposited 2023-07-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 9–21（13 aa）
Not recorded ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M MES monohydrate pH 6.5 (NaOH), 20% w/v PEG 4,000
Resolution 1.76 Å R-free 0.230
8TXV Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 1) Deposited 2023-08-24 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8TXW Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 2) Deposited 2023-08-24 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8TXX Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 3) Deposited 2023-08-24 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8U13 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 1) Deposited 2023-08-30 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8U14 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 2) Deposited 2023-08-30 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8U9S Cryo-EM structure of NRCAM nucleosome aided by scFv Deposited 2023-09-20 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8UBJ Cryo-EM structure of NRCAM nucleosome aided by scFv (3D Flex map) Deposited 2023-09-23 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8UBK Cryo-EM structure of Ascl1/E12a in complex with NRCAM nucleosome Deposited 2023-09-23 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8UBL Cryo-EM structure of Ascl1/E12a in complex with NRCAM nucleosome (3D Flex map) Deposited 2023-09-23 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8UPF Cryo-EM structure of the human nucleosome core particle in complex with RNF168-UbcH5c Deposited 2023-10-22 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8VFX Cryo-EM structure of 186bp ALBN1 nucleosome aided by scFv Deposited 2023-12-22 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.65 Å
8VFY Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 1) Deposited 2023-12-22 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.89 Å
8VFZ Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 2) Deposited 2023-12-22 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8VG0 Cryo-EM structure of GATA4 in complex with ALBN1 nucleosome Deposited 2023-12-22 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
8VG1 Cryo-EM structure of FoxA1 and GATA4 in complex with ALBN1 nucleosome Deposited 2023-12-22 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.48 Å
8VG2 Cryo-EM structure of FoxA1 and GATA4 in complex with H14 chromatosome Deposited 2023-12-22 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
8VLR Cryo-EM structure of native H2AK119bu nucleosome at 2.6 Deposited 2024-01-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 20–103（84 aa）
Chain F 20–103（84 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Tris-HCl, pH 7.5, 50 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8VMJ H3K4me3 nucleosome bound to PRC2_AJ119-450 Deposited 2024-01-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain J 1–103（103 aa）
Chain Q 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8VMN H3K4me3 nucleosome bound to PRC2_AJ1-450 Deposited 2024-01-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain J 1–103（103 aa）
Chain Q 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8VO0 H3K36me3-modified nucleosome bound to PRC2_AJ1-450 with histone H3 tail disengaged Deposited 2024-01-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain J 26–103（78 aa）
Chain Q 25–103（79 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8VOB H3K36me3-modified nucleosome bound to PRC2_AJ1-450 Deposited 2024-01-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain J 1–103（103 aa）
Chain Q 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8VWS Nucleosome containing 8oxoG at SHL-6 Deposited 2024-02-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；50 mM HEPES (pH-7.1), 100 mM NaCl, 1 mM TCEP, and 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8VWT OGG1 bound to a nucleosome containing 8oxoG at SHL-6 (composite map) Deposited 2024-02-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；50 mM HEPES (pH-7.1), 100 mM NaCl, 1 mM TCEP, and 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8VWU Nucleosome containing 8oxoG at SHL4 Deposited 2024-02-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；50 mM HEPES (pH-7.1), 100 mM NaCl, 1 mM TCEP, and 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8VWV OGG1 bound to a nucleosome containing 8oxoG at SHL4 (composite map) Deposited 2024-02-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；50 mM HEPES (pH-7.1), 100 mM NaCl, 1 mM TCEP, and 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8W9D Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 1 Deposited 2023-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 7 K POTASSIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8W9E Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 2 Deposited 2023-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 7 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8W9F Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 3 Deposited 2023-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8WG5 Cryo-EM structure of USP16 bound to H2AK119Ub nucleosome Deposited 2023-09-20 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 24–102（79 aa）
Chain F 24–102（79 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
8X15 Structure of nucleosome-bound SRCAP-C in the apo state Deposited 2023-11-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain D 1–103（103 aa）
Chain H 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8X19 Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state Deposited 2023-11-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain D 1–103（103 aa）
Chain H 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 7 MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8X1C Structure of nucleosome-bound SRCAP-C in the ADP-bound state Deposited 2023-11-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain D 1–103（103 aa）
Chain H 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 7 ATP ADENOSINE-5'-TRIPHOSPHATE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8X7I Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by intein-based E2-Ub-NCP conjugation strategy Deposited 2023-11-24 Different construct Different oligomeric state Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 20–102（83 aa）
Chain F 20–102（83 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
8X7J Cryo-EM structures of RNF168/UbcH5c-Ub/nucleosomes complex determined by activity-based chemical trapping strategy Deposited 2023-11-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 21–102（82 aa）
Chain F 21–102（82 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
8XBT The cryo-EM structure of the octameric RAD51 ring bound to the nucleosome with the linker DNA binding Deposited 2023-12-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.12 Å
8XBU The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome with the linker DNA binding Deposited 2023-12-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.24 Å
8XBW The cryo-EM structure of the RAD51 N-terminal lobe domain bound to the histone H4 tail of the nucleosome Deposited 2023-12-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.89 Å
8XRJ RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei Deposited 2024-01-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain b 2–103（102 aa）
Chain f 2–103（102 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8XVS RNA polymerase II elongation complex with downstream nucleosome extracted from human nuclei Deposited 2024-01-15 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain b 2–103（102 aa）
Chain f 2–103（102 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8Y3C Cryo-EM structure of the overlapping di-nucleosome (closed form) Deposited 2024-01-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.21 Å
8Y3D Cryo-EM structure of the overlapping di-nucleosome (intermediate form2) Deposited 2024-01-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
8Y3E Cryo-EM structure of the overlapping di-nucleosome (open form) Deposited 2024-01-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.32 Å
8Y3F Cryo-EM structure of the overlapping di-nucleosome (intermediate form1) Deposited 2024-01-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.54 Å
8YBJ Cryo-EM structure of human nucleosome core particle composed of the Widom 601 DNA sequence Deposited 2024-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.38 Å
8YBK Cryo-EM structure of the human nucleosome containing the H3.1 E97K mutant Deposited 2024-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.69 Å
8YE8 Crystal structure of mouse BAHCC1 TTD domain in complex with H4K20me1 peptide Deposited 2024-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 15–26（12 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM MES, pH 6.5, 10 mM Li2SO4, 8% PEG20000 and 3 mM H4K20me
Resolution 1.90 Å R-free 0.238
8YJF Structure of human SPT16 MD-CTD and MCM2 HBD chaperoning a histone H3-H4 tetramer and an H2A-H2B dimer Deposited 2024-03-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain D 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1 M calcium acetate, 0.1 M Sodium cacodylate pH 5.5, 12% (w/v) PEG 8000
Resolution 4.40 Å R-free 0.312
8YJM Structure of human SPT16 MD-CTD and MCM2 HBD chaperoning a histone H3-H4 tetramer and a single chain H2B-H2A chimera Deposited 2024-03-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric
Chain D 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.2 M sodium acetate, 0.1 M sodium citrate pH 5.5, 5%(w/v) PEG 4000
Resolution 4.15 Å R-free 0.286
8YNY Structure of Cas9-sgRNA ribonucleoprotein bound to nucleosome Deposited 2024-03-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: 13-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.52 Å
8YTI Crystal Structure of Nucleosome-H1x Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2024-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded CL CHLORIDE ION × 8 CA CALCIUM ION × 52 K POTASSIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45 mM CaCl2, 25 mM KCl, 10 mM Na-acetate (pH 4.5)
Resolution 2.70 Å R-free 0.267
8YV8 Cryo-EM structure of CDCA7 bound to nucleosome including hemimethylated CpG site in Widom601 positioning sequence. Deposited 2024-03-28 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8Z50 Crystal structure of the ASF1-H3T-H4 complex Deposited 2024-04-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1.0 M Lithium chloride, 0.1 M MES pH 6.0, 10% PEG 6000
Resolution 2.80 Å R-free 0.255
8ZJR Structure of nucleosome-bound RFX5 complex Deposited 2024-05-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8ZJT Structure of free nucleosome Deposited 2024-05-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9BE6 Cryo-EM structure of Human Nucleosome collected by Leginon on Krios at 3.0 Angstrom resolution Deposited 2024-04-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain F 26–103（78 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9D3K Two Dsup molecules in complex with the nucleosome open from both sides Deposited 2024-08-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 24–102（79 aa）
Chain F 24–102（79 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
9D3L Two Dsup molecules in complex with the nucleosome open from the left side Deposited 2024-08-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 24–102（79 aa）
Chain F 24–102（79 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9D3M Two HMGN2s in complex with the nucleosome Deposited 2024-08-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 22–103（82 aa）
Chain F 22–103（82 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9D3N 167-bp 5S rDNA nucleosome cross-linked with glutaraldehyde Deposited 2024-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 25–103（79 aa）
Chain F 25–103（79 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9D3O 167-bp 5S rDNA nucleosome - closed Deposited 2024-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 22–103（82 aa）
Chain F 22–103（82 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9D3P 167-bp 5S rDNA nucleosome - open I (open only on the downstream side) Deposited 2024-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 22–103（82 aa）
Chain F 22–103（82 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
9D3Q 167-bp 5S rDNA nucleosome - open II Deposited 2024-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 23–103（81 aa）
Chain F 23–103（81 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9D3R 147-bp 5S rDNA nucleosome - closed Deposited 2024-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 22–103（82 aa）
Chain F 22–103（82 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9D3S 147-bp 5S rDNA nucleosome - open I (open on the downstream side) Deposited 2024-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 22–103（82 aa）
Chain F 22–103（82 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9D3T 147-bp 5S rDNA nucleosome cross-linked with glutaraldehyde Deposited 2024-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 25–102（78 aa）
Chain F 25–102（78 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9DWF Nucleosome containing a 1-nt gap at SHL-4.5 Deposited 2024-10-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9DWG DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 1, composite) Deposited 2024-10-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9DWH DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 2, composite) Deposited 2024-10-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9DWI DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 3, composite) Deposited 2024-10-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9DWJ Nucleosome containing a 1-nt gap at SHL-3.5 Deposited 2024-10-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9DWK DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-3.5 Deposited 2024-10-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
9DWL Nucleosome containing a 1-nt gap at SHL-5.5 Deposited 2024-10-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
9DWM DNA polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-5.5 Deposited 2024-10-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9E00 Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Deposited 2024-10-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain N 1–103（103 aa）
Chain R 1–103（103 aa）
Not recorded ZN ZINC ION × 9 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.75 Å
9E05 The consensus model of the cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Deposited 2024-10-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain N 1–103（103 aa）
Chain R 1–103（103 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.00 Å
9E09 Cryo-EM structure a single nucleosome (2) focus of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Deposited 2024-10-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain N 1–103（103 aa）
Chain R 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.72 Å
9E0R Cryo-EM structure of a single nucleosome (1) focus of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Deposited 2024-10-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9E2D Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to a di-nucleosome with a five base pair linker Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain N 1–103（103 aa）
Chain R 1–103（103 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.08 Å
9E2F Cryo-EM structure of a di-nucleosome with a five base pair linker Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain N 1–103（103 aa）
Chain R 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.90 Å
9E2Q Cryo-EM structure of DNMT 3A2/3B3 tetramer in complex with a di-nucleosome with a six base pair linker Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain N 1–103（103 aa）
Chain R 1–103（103 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.14 Å
9E2R Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to a di-nucleosome and an histone-3 peptide Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain N 1–103（103 aa）
Chain R 1–103（103 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.71 Å
9E3D Cryo-EM structure of DNMT 3A2/3B3 tetramer in complex with a di-nucleosome with K120R mutant H2B Deposited 2024-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain N 1–103（103 aa）
Chain R 1–103（103 aa）
Not recorded ZN ZINC ION × 9 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9E3R Cryo-EM structure of PWWP domain deleted DNMT 3A2/3B3 in complex with a di-nucleosome Deposited 2024-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain N 1–103（103 aa）
Chain R 1–103（103 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
9E3U Cryo-EM structure of DNMT 3A2/3B3 tetramer bound to a di-nucleosome with a 25 base-pair linker Deposited 2024-10-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 9 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.90 Å
9E49 Cryo-EM structure of a di-nucleosome with an eight base-pair linker Deposited 2024-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain N 1–103（103 aa）
Chain R 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.93 Å
9ECP Structure of the native human NCP purified from HEK293 cells Deposited 2024-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 22–103（82 aa）
Chain F 22–103（82 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.91 Å
9EOZ Human OGG1 bound to a nucleosome core particle with 8-oxodGuo lesion at SHL6.0 Deposited 2024-03-16 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9FGQ Structure of human APC3loop 375-381 bound to the NCP Deposited 2024-05-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM HEPEs pH8.0, 50 mM NaCl, 0.5 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
9FH9 Structure of CyclinB1 N-terminus bound to the NCP Deposited 2024-05-27 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
9GCG CryoEM structure of the human INO80 core- H2A.Z nucleosome complex Deposited 2024-08-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain N 2–103（102 aa）
Chain R 2–103（102 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 7 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.43 Å
9GE4 CryoEM structure of the human INO80 core- H2A.Z nucleosome complex Deposited 2024-08-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain N 2–103（102 aa）
Chain R 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.52 Å
9GE5 CryoEM structure of the human INO80-Hexasome complex Deposited 2024-08-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain N 23–103（81 aa）
Chain R 26–103（78 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
9GEL CryoEM structure of the human INO80-Hexasome complex Deposited 2024-08-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain N 2–103（102 aa）
Chain R 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.86 Å
9GEV CryoEM structure of the human INO80 core-nucleosome complex state N-6 Deposited 2024-08-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain N 2–103（102 aa）
Chain R 2–103（102 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
9GF6 CryoEM structure of the human INO80 core-nucleosome complex state N-6 Deposited 2024-08-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain N 2–103（102 aa）
Chain R 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9GFB CryoEM structure of the human INO80 core-nucleosome complex state N-7 Deposited 2024-08-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain N 2–103（102 aa）
Chain R 2–103（102 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 6 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
9GFM CryoEM structure of the human INO80 core-nucleosome complex state N-7 Deposited 2024-08-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain N 22–103（82 aa）
Chain R 25–103（79 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9GMK SIRT7:H3K18DTU nucleosome complex Deposited 2024-08-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9GMR SIRT7-H3K36MTUnucleosome complex Deposited 2024-08-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded A1IY0 [[(2~{R},3~{a}~{R},5~{R},6~{R},6~{a}~{R})-2-(methylamino)-6-oxidanyl-2-(propylamino)-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxathiol-5-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9GW2 State 2 MAP 1 SETD2 bound to proximal H3 of upstream nucleosome Deposited 2024-09-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.84 Å
9GXA CENP-A/H4 di-tetrasome assembled on alpha-satellite DNA. Deposited 2024-09-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain D 2–103（102 aa）
Chain F 2–103（102 aa）
Chain H 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.01 Å
9IGW Ku70/80 bound to 147 bp nucleosome Deposited 2025-02-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å
9IGX Ku70/80 bound to 153 bp nucleosome Deposited 2025-02-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain B 18–101（84 aa）
Chain F 18–101（84 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.56 Å
9II7 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome containing histone variant H2A.B Deposited 2024-06-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9IPU cryo-EM structure of the RNF168(1-193)/UbcH5c-Ub ubiquitylation module bound to H1.0-K63-Ub3 modified chromatosome Deposited 2024-07-11 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
9J0N Paused elongation complex of mammalian RNA polymerase II with nucleosome (PEC2-nuc) Deposited 2024-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 27 PDB declaration: 30-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9J0O Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC1-nuc) Deposited 2024-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9J0P Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC2-nuc) Deposited 2024-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9J8M Cryo-EM structure of BAF-Lamin A/C IgF-nucleosome complex (High mobility complex) Deposited 2024-08-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.82 Å
9J8N Cryo-EM structure of BAF-Lamin A/C IgF-nucleosome complex (Low mobility complex) Deposited 2024-08-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 32-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.14 Å
9J8O Cryo-EM structure of BAF-Lamin A/C IgF-H1-nucleosome complex Deposited 2024-08-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 28-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.05 Å
9J8W Cryo-EM structure of NCP-UV-DDB complex containing CPD Deposited 2024-08-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.38 Å
9JC6 Human H2BW2 nucleosome Deposited 2024-08-28 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.34 Å
9K9L Cryo-EM structure of the human CENP-A-H4 octasome. Deposited 2024-10-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain D 1–103（103 aa）
Chain F 1–103（103 aa）
Chain H 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.66 Å
9KQO cryo-EM structure of RNF20/RNF40-RAD6A-Ub in complex with H2BS112GlcNAc nucleosome Deposited 2024-11-26 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain F 2–103（102 aa）
Chain L 2–103（102 aa）
Not recorded ZN ZINC ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.48 Å
9L1X hDEK-nucleosome complex (conformation 1) Deposited 2024-12-16 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded UNX UNKNOWN LIGAND × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.69 Å
9L22 hDEK-nucleosome complex (conformation 2) Deposited 2024-12-16 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded UNX UNKNOWN LIGAND × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9MLL GammaH2AX containing nucleosomes, Parallel stack Deposited 2024-12-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain M 1–103（103 aa）
Chain Q 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9MLN GammaH2AX containing nucleosome, Canonical (Class 1) Deposited 2024-12-19 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9MLR GammaH2AX containing nucleosome, Half-wrapped (Class 2) Deposited 2024-12-19 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9MLS GammaH2AX containing nucleosome, Extended (Class 3) Deposited 2024-12-19 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9MMK H2AX containing nucleosome, Canonical (Class 1) Deposited 2024-12-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9MMM H2AX containing nucleosomes, Parallel stack Deposited 2024-12-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain M 1–103（103 aa）
Chain Q 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
9MMN H2AX containing nucleosomes, Left offset stack Deposited 2024-12-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain M 1–103（103 aa）
Chain Q 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9MMO H2AX containing nucleosomes, Right offset stack Deposited 2024-12-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain M 1–103（103 aa）
Chain Q 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
9MMT H2AX containing nucleosome, Unwrapped (Class 2) Deposited 2024-12-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9NQU KDM6B-nucleosome structure stabilized by H3K27C-UNC8015 covalent conjugate Deposited 2025-03-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded FE FE (III) ION × 1 ZN ZINC ION × 1 OH0 N-heptanoyl-N-hydroxy-beta-alanine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.16 Å
9OGR Cryo-EM analysis of human H2A.Z on methylated Sat2R-P DNA (v1) Deposited 2025-05-01 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.78 Å
9OGS Cryo-EM analysis of human H2A.Z on Sat2R-P DNA (v1) Deposited 2025-05-01 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
9OGZ Cryo-EM analysis of human H2A.Z on Sat2R-P DNA (v2) Deposited 2025-05-02 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
9OH0 Cryo-EM analysis of human H2A.Z on methylated Sat2R-P DNA (v2) Deposited 2025-05-02 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.78 Å
9OH1 Cryo-EM analysis of human H2A.Z on 601L DNA Deposited 2025-05-02 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
9OH2 Cryo-EM analysis of human H2A.Z on methylated 601L DNA Deposited 2025-05-02 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.14 Å
9Q80 Ku70/80 with Ku70 linker and SAP domain bound to a 153 bp H2AX nucleosome Deposited 2025-02-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
9Q8X Ku70/80 bound to a 153 bp H2AX nucleosome Deposited 2025-02-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
9Q9F DNA-PK bound to a 153 bp H2AX nucleosome model 1 Deposited 2025-02-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.54 Å
9QCR DNA-PK bound to 153 bp H2AX nucleosome model 2 Deposited 2025-03-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.37 Å
9QCS Ku80 mediated DNA-PK dimer bound to 153 bp H2AX nucleosome Deposited 2025-03-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 26-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.38 Å
9QMS DNA-PK bound to 153 bp H2AX nucleosome with ATPyS Deposited 2025-03-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 30-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.00 Å
9R04 p53 bound to the nucleosome at position SHL-5.7 (crosslinked sample) Deposited 2025-04-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9R2M p53 bound to nucleosome at position SHL+5.9 (non-crosslinked sample, composite map) Deposited 2025-04-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9R2P p53 bound to nucleosome at position SHL+5.9 (crosslinked sample) Deposited 2025-04-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.18 Å
9R2Q p53 bound to nucleosome at position SHL-5.7 (non-crosslinked sample) Deposited 2025-04-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9RL4 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL-6 Deposited 2025-06-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded PTD PENTANEDIAL × 16 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9RMC Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 1 Deposited 2025-06-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9RN1 Structure of BAF-nucleosome complex with OCT4-SOX2 at SHL+6 in ADP-bound state, BAF47 bound to ATPase lobe 2 Deposited 2025-06-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.90 Å
9RN2 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 2 Deposited 2025-06-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 19 PDB declaration: 21-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
9RZC State 3 MAP 1 SETD2 bound to distal H3 of upstream nucleosome Deposited 2025-07-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.66 Å
9RZE State 2 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to proximal upstream H3 Deposited 2025-07-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.53 Å
9S0U State 3 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to distal upstream H3 Deposited 2025-07-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.72 Å
9S3G State 1 MAP3 RNA Pol II activated elongation complex with SETD2 and upstream hexasome Deposited 2025-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
9TAX Structure of the human inner kinetochore CCAN bound to a mono-CENP-A nucleosome Deposited 2025-11-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain d 1–103（103 aa）
Chain h 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
9TAY Structure of the human inner kinetochore CCAN bound to a di-CENP-A nucleosome Deposited 2025-11-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 35 PDB declaration: 37-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain d 1–103（103 aa）
Chain h 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 15.50 Å
9U5U The 1:1 cryo-EM structure of BAP1/ASXL1-K351Ub in complex with H2AK119Ub nucleosome Deposited 2025-03-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
9UJS RNA polymerase II elongation complex stalled at SHL(-4) of the H3-H4 octasome Deposited 2025-04-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain b 1–103（103 aa）
Chain d 1–103（103 aa）
Chain f 1–103（103 aa）
Chain h 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
9UJT RNA polymerase II elongation complex stalled at SHL(-0.5) of the H3-H4 octasome (tetrasome) Deposited 2025-04-17 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain f 1–103（103 aa）
Chain h 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.54 Å
9UZ7 Cryo-EM structure of the nucleosome core particle with site-specific DNA-histone crosslinking Deposited 2025-05-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–103（102 aa）
Chain D 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；10 mM HEPES, pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution not provided
9V6Q Cryo-EM structure of two cPRC1 complexes bound to opposite faces of an endogenous 147-bp mono-nucleosome Deposited 2025-05-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 4.60 Å
9V6S Cryo-EM structure of a single cPRC1 complex engaged on one face of an endogenous 147-bp mononucleosome Deposited 2025-05-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.00 Å
9V6X Cryo-EM structure of the cPRC1 complex bound to an endogenous 184-bp mono-nucleosome Deposited 2025-05-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 4.00 Å
9V8L Cryo-EM structure of the cPRC1-di-nucleosome (loose) complex Deposited 2025-05-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain S 1–103（103 aa）
Chain T 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 6.60 Å
9V9H Cryo-EM structure of the cPRC1-di-nucleosome (tight) complex Deposited 2025-05-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain Q 1–103（103 aa）
Chain R 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 4.50 Å
9V9P Cryo-EM structure of the cPRC1-di-nucleosome (CBX7) complex Deposited 2025-06-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain Q 1–103（103 aa）
Chain R 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.40 Å
9WMS Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type B) Deposited 2025-09-03 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9WMT Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type A) Deposited 2025-09-03 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
9WMU Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type A) Deposited 2025-09-03 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.28 Å
9WMV Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type B) Deposited 2025-09-03 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.66 Å
9WMW Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, FACT-hexamer) Deposited 2025-09-03 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
9XSF Cryo-EM structure of H4S47GlcNAc nucleosome at 3.39 angstrom Deposited 2025-11-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.39 Å
9Y46 Human nucleosome structure on Nickel-NTA lipid affinity grid (C2 refinement) Deposited 2025-09-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.59 Å
9Y47 Human nucleosome structure on Nickel-NTA lipid affinity grid (C1 refinement) Deposited 2025-09-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.74 Å
9YL3 State 1 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.50 Å
9YLE State 3 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.63 Å
9YLY MLL4FC bound to a nucleosome with p53 RE Deposited 2025-10-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 14 PDB declaration: 16-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.77 Å
9YM8 State 2 focused on PHD FYR of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.43 Å
9YMF State 2 focused on H3 N terminal tail of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.45 Å
9ZEN Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1B2 Deposited 2025-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain B 25–103（79 aa）
Chain F 25–103（79 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES pH7.6, 50 mM NaCl, 0.5 mM MgCl2, 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.17 Å
9ZEO Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1G1 Deposited 2025-11-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 21–103（83 aa）
Chain F 21–103（83 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES pH7.6, 50 mM NaCl, 0.5 mM MgCl2, 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å

581 other PDB entries and 633 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H4_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–82； UniProt 21–102 Author chain F； PDBConstruct 1–82； UniProt 21–102

Histone H2A type 1-B/E

Homo sapiens

UniProt P04908

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 10 DNA 2 PDB declaration: dodecameric（12） Consistent with all polymer counts Chain C； UniProt 15–119 Chain G； UniProt 11–118 Not recorded Histone H3.2 × 2 （Q71DI3） Histone H4 × 2 （P62805） Histone H2B type 1-K × 2 （O60814） DNA (143-MER) × 1 DNA (143-MER) × 1 Ubiquitin-conjugating enzyme E2 D3 × 1 （P61077） E3 ubiquitin-protein ligase RNF168 × 1 （Q8IYW5） ZN ZINC ION × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.27 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8X7K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2RVQ Solution structure of the isolated histone H2A-H2B heterodimer Deposited 2016-03-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–130（130 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；293 K；Ionic strength (raw mmCIF value) 400；Pressure ambient
NMR sample composition 0.1-0.3 mM [U-13C; U-15N; U-2H] entity_1-1, 0.1-0.3 mM [U-13C; U-15N; U-2H] entity_2-2, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
3A6N The nucleosome containing a testis-specific histone variant, human H3T Deposited 2009-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.70 Å R-free 0.264
3AFA The human nucleosome structure Deposited 2010-02-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.270
3AN2 The structure of the centromeric nucleosome containing CENP-A Deposited 2010-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.60 Å R-free 0.325
3AV1 The human nucleosome structure containing the histone variant H3.2 Deposited 2011-02-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.290
3AV2 The human nucleosome structure containing the histone variant H3.3 Deposited 2011-02-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.272
3AYW Crystal Structure of Human Nucleosome Core Particle Containing H3K56Q mutation Deposited 2011-05-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.90 Å R-free 0.273
3AZE Crystal Structure of Human Nucleosome Core Particle Containing H3K64Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.00 Å R-free 0.302
3AZF Crystal Structure of Human Nucleosome Core Particle Containing H3K79Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.70 Å R-free 0.263
3AZG Crystal Structure of Human Nucleosome Core Particle Containing H3K115Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.40 Å R-free 0.269
3AZH Crystal Structure of Human Nucleosome Core Particle Containing H3K122Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 3 MN MANGANESE (II) ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.49 Å R-free 0.266
3AZI Crystal Structure of Human Nucleosome Core Particle Containing H4K31Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.70 Å R-free 0.289
3AZJ Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.89 Å R-free 0.268
3AZK Crystal Structure of Human Nucleosome Core Particle Containing H4K59Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.20 Å R-free 0.258
3AZL Crystal Structure of Human Nucleosome Core Particle Containing H4K77Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.70 Å R-free 0.259
3AZM Crystal Structure of Human Nucleosome Core Particle Containing H4K79Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 3 MN MANGANESE (II) ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.89 Å R-free 0.296
3AZN Crystal Structure of Human Nucleosome Core Particle Containing H4K91Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.00 Å R-free 0.254
3W96 Crystal Structure of Human Nucleosome Core Particle lacking H2A N-terminal region Deposited 2013-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 11–130（120 aa） Fragment：UNP residues 11-130
Chain G 11–130（120 aa） Fragment：UNP residues 11-130
Not recorded CL CHLORIDE ION × 1 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.00 Å R-free 0.296
3W97 Crystal Structure of Human Nucleosome Core Particle lacking H2B N-terminal region Deposited 2013-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.20 Å R-free 0.321
3W98 Crystal Structure of Human Nucleosome Core Particle lacking H3.1 N-terminal region Deposited 2013-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.42 Å R-free 0.303
3W99 Crystal Structure of Human Nucleosome Core Particle lacking H4 N-terminal region Deposited 2013-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.00 Å R-free 0.312
3WKJ The nucleosome containing human TSH2B Deposited 2013-10-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.291
3WTP Crystal Structure of the heterotypic nucleosome containing human CENP-A and H3.3 Deposited 2014-04-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, vapor diffusion, hanging drop, temperature 293K
Resolution 2.67 Å R-free 0.270
3X1S Crystal structure of the nucleosome core particle Deposited 2014-11-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded MN MANGANESE (II) ION × 6 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；60-70mM KCL, 70-90mM MnCl2, 24% MPD, 20mM Na-Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.81 Å R-free 0.270
3X1V Crystal structure of nucleosome core particle in the presence of histone variant involved in reprogramming Deposited 2014-11-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded MN MANGANESE (II) ION × 19 CL CHLORIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；60-70 mM KCl, 70-90 mM MnCl2, Na-cocodylate, 24% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.92 Å R-free 0.259
4YM5 Crystal structure of the human nucleosome containing 6-4PP (inside) Deposited 2015-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 4.00 Å R-free 0.289
4YM6 Crystal structure of the human nucleosome containing 6-4PP (outside) Deposited 2015-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 3.51 Å R-free 0.287
4Z5T The nucleosome containing human H3.5 Deposited 2015-04-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.80 Å R-free 0.269
5AV5 human nucleosome core particle Deposited 2015-06-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions LIQUID DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.40 Å R-free 0.233
5AV6 human nucleosome core particle Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.20 Å R-free 0.229
5AV8 human nucleosome core particle Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.20 Å R-free 0.233
5AV9 human nucleosome core particle Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.20 Å R-free 0.239
5AVB human nucleosome core particle Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.40 Å R-free 0.236
5AVC human nucleosome core particle Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.40 Å R-free 0.238
5AY8 Crystal structure of human nucleosome containing H3.Y Deposited 2015-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 8 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；sodium acetate, manganese chloride, 2-propanol, trimethylamine N-oxide
Resolution 2.80 Å R-free 0.249
5B0Y Crystal structure of the nucleosome containing histone H3 with the crotonylated lysine 122 Deposited 2015-11-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.56 Å R-free 0.249
5B0Z The crystal structure of the nucleosome containing H3.2, at 1.98 A resolution Deposited 2015-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 1.99 Å R-free 0.254
5B24 The crystal structure of the nucleosome containing cyclobutane pyrimidine dimer Deposited 2015-12-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 3.60 Å R-free 0.249
5B2I Human nucleosome containing CpG unmethylated DNA Deposited 2016-01-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 3.00 Å R-free 0.257
5B2J Human nucleosome containing CpG methylated DNA Deposited 2016-01-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.60 Å R-free 0.252
5B31 The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.1. Deposited 2016-02-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 8 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.20 Å R-free 0.271
5B32 The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.3. Deposited 2016-02-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.35 Å R-free 0.259
5B40 The nucleosome structure containing H2B-K120 and H4-K31 monoubiquitinations Deposited 2016-03-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；90mM Tris-HCl (pH 7.8), 3.6% PGA-LM, 25.2% PEG 400, 2-6% Pentaerythritol ethoxylate (3/4 EO/OH)
Resolution 3.33 Å R-free 0.263
5CPI Nucleosome containing unmethylated Sat2R DNA Deposited 2015-07-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.90 Å R-free 0.295
5CPJ Nucleosome containing methylated Sat2R DNA Deposited 2015-07-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 3.15 Å R-free 0.295
5CPK Nucleosome containing methylated Sat2L DNA Deposited 2015-07-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.63 Å R-free 0.284
5GSE Crystal structure of unusual nucleosome Deposited 2016-08-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；potassium bromide, potassium thiocyanate, Tris-HCl, PGA-LM, PEG 400
Resolution 3.14 Å R-free 0.255
5GTC Crystal structure of complex between DMAP-SH conjugated with a Kaposi's sarcoma herpesvirus LANA peptide (5-15) and nucleosome core particle Deposited 2016-08-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.70 Å R-free 0.267
5GXQ The crystal structure of the nucleosome containing H3.6 Deposited 2016-09-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.85 Å R-free 0.262
5JRG Crystal structure of the nucleosome containing the DNA with tetrahydrofuran (THF) Deposited 2016-05-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.50 Å R-free 0.245
5VEY Solution NMR structure of histone H2A-H2B mono-ubiquitylated at H2A Lys15 in complex with RNF169 (653-708) Deposited 2017-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 13–106（94 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 50 mM KCl；Pressure 1
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 50 mM KCl；Pressure 1
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
Resolution not provided
5X7X The crystal structure of the nucleosome containing H3.3 at 2.18 angstrom resolution Deposited 2017-02-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.18 Å R-free 0.256
5XF3 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,R-configuration) Deposited 2017-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 1 RUD [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 × 2 RRK (1R,2R)-1,2-diphenylethane-1,2-diamine × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；35-55 mM MnCl2, 25-49 mM KCl, 20 mM K-Cacodylate pH 6.0
Resolution 2.60 Å R-free 0.270
5XF4 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (S,S-configuration) Deposited 2017-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 1 RUD [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 × 2 SSK (1S,2S)-1,2-diphenylethane-1,2-diamine × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；35-55 mM MnCl2, 25-49 mM KCl, 20 mM K-Cacodylate pH 6.0
Resolution 2.87 Å R-free 0.266
5XF5 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,S-configuration) Deposited 2017-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 1 RUD [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 × 2 RSK (1S,2R)-1,2-diphenylethane-1,2-diamine × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；35-55mM MnCl2, 25-49mM KCl, 20mM K-Cacodylate pH 6.0
Resolution 2.82 Å R-free 0.264
5Y0C Crystal Structure of the human nucleosome at 2.09 angstrom resolution Deposited 2017-07-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 10 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.09 Å R-free 0.249
5Y0D Crystal Structure of the human nucleosome containing the H2B E76K mutant Deposited 2017-07-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 1.99 Å R-free 0.252
5Z23 Crystal structure of the nucleosome containing a chimeric histone H3/CENP-A CATD Deposited 2017-12-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Mutation：L51M,L58M,L93M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L51M,L58M,L93M Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.73 Å R-free 0.261
5ZBX The crystal structure of the nucleosome containing histone H3.1 CATD(V76Q, K77D) Deposited 2018-02-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.58 Å R-free 0.249
6A5L RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA Deposited 2018-06-24 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.60 Å
6A5O RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome Deposited 2018-06-25 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.90 Å
6A5P RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome Deposited 2018-06-25 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å
6A5R RNA polymerase II elongation complex stalled at SHL(-2) of the nucleosome Deposited 2018-06-25 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
6A5T RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome Deposited 2018-06-25 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.70 Å
6A5U RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation Deposited 2018-06-25 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
6BUZ Cryo-EM structure of CENP-A nucleosome in complex with kinetochore protein CENP-N Deposited 2017-12-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.92 Å
6E0C Cryo-EM structure of the CENP-A nucleosome (W601) in complex with a single chain antibody fragment Deposited 2018-07-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.63 Å
6E0P Cryo-EM structure of the centromeric nucleosome (Native alpha satellite DNA) in complex with a single chain antibody fragment Deposited 2018-07-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；blot for 2.5 sec before plunging
Resolution 2.60 Å
6HKT Structure of an H1-bound 6-nucleosome array Deposited 2018-09-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 48 PDB declaration: 50-meric
Chain 0 1–130（130 aa）
Chain 2 1–130（130 aa）
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain W 1–130（130 aa）
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Chain m 1–130（130 aa）
Chain q 1–130（130 aa）
Chain w 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；293.15 K；15% MPD, 0.1 M NaCl and 0.1 M Tris pH 8.8
Resolution 9.70 Å R-free 0.286
6HTS Cryo-EM structure of the human INO80 complex bound to nucleosome Deposited 2018-10-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain K 1–130（130 aa）
Chain O 1–130（130 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
6INQ RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position) Deposited 2018-10-26 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
6IPU Human nucleosome core particle containing 145 bp of DNA Deposited 2018-11-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 14–120（107 aa）
Chain G 14–120（107 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；manganese chloride, potassium chloride, potassium cacodylate
Resolution 1.99 Å R-free 0.263
6IQ4 Nucleosome core particle cross-linked with a hetero-binuclear molecule possessing RAPTA and gold(I) 4-(diphenylphosphino)benzoic acid groups. Deposited 2018-11-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 15–120（106 aa）
Chain G 15–120（106 aa）
Not recorded AU GOLD ION × 1 XIS 4-diphenylphosphanylbenzoic acid × 1 MG MAGNESIUM ION × 4 D0X [Ru(eta(6)-p-cymene)Cl-2(pta) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；manganese chloride, potassium chloride, potassium cacodylate
Resolution 2.25 Å R-free 0.257
6IR9 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome Deposited 2018-11-12 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6J4W RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-5) of the nucleosome Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.90 Å
6J4X RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1A) Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Y RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1B) Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Z RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6J50 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome (tilted conformation) Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
6J51 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome, weak Elf1 (+1 position) Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6JR0 Crystal structure of the human nucleosome phased with 12 selenium atoms Deposited 2019-04-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Mutation：L65M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L65M Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.50 Å R-free 0.253
6JR1 Crystal structure of the human nucleosome phased with 16 selenium atoms Deposited 2019-04-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Mutation：L65M, L85M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L65M, L85M Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.40 Å R-free 0.243
6JXD Human nucleosome core particle with cohesive end DNA termini Deposited 2019-04-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 14–119（106 aa）
Chain G 14–119（106 aa）
Not recorded MN MANGANESE (II) ION × 17 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；manganese chloride, potassium chloride, potassium cacodylate
Resolution 2.25 Å R-free 0.292
6KE9 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-07-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 15–119（105 aa）
Chain G 15–119（105 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
Resolution 2.22 Å R-free 0.230
6KXV Crystal structure of a nucleosome containing Leishmania histone H3 Deposited 2019-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；sodium acetate, isopropanol, manganese chloride, trimethylamine N-oxide
Resolution 3.63 Å R-free 0.264
6L49 H3-CA-H3 tri-nucleosome with the 22 base-pair linker DNA Deposited 2019-10-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain U 1–130（130 aa）
Chain Y 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 18.90 Å
6L4A H3-H3-H3 tri-nucleosome with the 22 base-pair linker DNA Deposited 2019-10-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain U 1–130（130 aa）
Chain Y 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 12.30 Å
6L9H The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-11-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 15–119（105 aa）
Chain G 15–119（105 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
Resolution 2.60 Å R-free 0.278
6L9Z 338 bp di-nucleosome assembled with linker histone H1.X Deposited 2019-11-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CL CHLORIDE ION × 8 CA CALCIUM ION × 65 K POTASSIUM ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；Calcium chloride, Potassium chloride, Potassium Cacodylate
Resolution 2.50 Å R-free 0.256
6LA2 343 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 Deposited 2019-11-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 34 PDB declaration: 38-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain W 1–130（130 aa）
Chain a 1–130（130 aa）
Chain g 1–130（130 aa）
Chain k 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, Potassium chloride, Sodium acetate
Resolution 3.89 Å R-free 0.267
6LA8 349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 Deposited 2019-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CA CALCIUM ION × 23 K POTASSIUM ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate (cryo-25% MPD)
Resolution 3.40 Å R-free 0.265
6LA9 349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 (high cryoprotectant) Deposited 2019-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CA CALCIUM ION × 40 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
Resolution 3.70 Å R-free 0.266
6LAB 169 bp nucleosome, harboring cohesive DNA termini, assembled with linker histone H1.0 Deposited 2019-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CA CALCIUM ION × 20 K POTASSIUM ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
Resolution 3.20 Å R-free 0.262
6LE9 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-11-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 15–119（105 aa）
Chain G 15–119（105 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
Resolution 2.60 Å R-free 0.281
6LER 169 bp nucleosome harboring non-identical cohesive DNA termini. Deposited 2019-11-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CA CALCIUM ION × 6 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
Resolution 3.00 Å R-free 0.261
6LER 169 bp nucleosome harboring non-identical cohesive DNA termini. Deposited 2019-11-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CA CALCIUM ION × 8 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
Resolution 3.00 Å R-free 0.261
6M3V 355 bp di-nucleosome harboring cohesive DNA termini Deposited 2020-03-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded K POTASSIUM ION × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；291 K；Calcium chloride, Potassium chloride, Potassium Cacodylate, Poly glutamic acid
Resolution 4.60 Å R-free 0.261
6M44 355 bp di-nucleosome harboring cohesive DNA termini (high cryoprotectant) Deposited 2020-03-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；Calcium chloride, Potassium chloride, Potassium Cacodylate, Poly glutamic acid
Resolution 3.81 Å R-free 0.286
6O1D Cryo-EM structure of the centromeric nucleosome with native alpha satellite DNA Deposited 2019-02-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；blot for 2.5 sec before plunging
Resolution 3.40 Å
6R8Y Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB Deposited 2019-04-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6R8Z Cryo-EM structure of NCP_THF2(-1)-UV-DDB Deposited 2019-04-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6R90 Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A Deposited 2019-04-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6R91 Cryo-EM structure of NCP_THF2(-3)-UV-DDB Deposited 2019-04-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6R92 Cryo-EM structure of NCP-THF2(+1)-UV-DDB class B Deposited 2019-04-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
6R93 Cryo-EM structure of NCP-6-4PP Deposited 2019-04-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6R94 Cryo-EM structure of NCP_THF2(-3) Deposited 2019-04-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6T79 Structure of a human nucleosome at 3.2 A resolution Deposited 2019-10-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 3.20 Å
6T7A Structure of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 3.70 Å
6T7B Structure of human Sox2 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 5.10 Å
6T7C Structure of two copies of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 4.00 Å
6T7D Structure of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 4.40 Å
6T90 OCT4-SOX2-bound nucleosome - SHL-6 Deposited 2019-10-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded PTD PENTANEDIAL × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
6T93 Nucleosome with OCT4-SOX2 motif at SHL-6 Deposited 2019-10-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.49 Å
6V92 RSC-NCP Deposited 2019-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 33 PDB declaration: 35-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 20.00 Å
6YOV OCT4-SOX2-bound nucleosome - SHL+6 Deposited 2020-04-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded PTD PENTANEDIAL × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.42 Å
7BWD Structure of Dot1L-H2BK34ub Nucleosome Complex Deposited 2020-04-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.32 Å
7BXT The cryo-EM structure of CENP-A nucleosome in complex with CENP-C peptide and CENP-N N-terminal domain Deposited 2020-04-20 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7BY0 The cryo-EM structure of CENP-A nucleosome in complex with the phosphorylated CENP-C Deposited 2020-04-21 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7C0M Human cGAS-nucleosome complex Deposited 2020-05-01 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Chain c 2–130（129 aa）
Chain g 2–130（129 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7CCQ Structure of the 1:1 cGAS-nucleosome complex Deposited 2020-06-17 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 16–118（103 aa）
Chain G 16–118（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7CCR Structure of the 2:2 cGAS-nucleosome complex Deposited 2020-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain C 16–118（103 aa）
Chain G 16–118（103 aa）
Chain N 16–118（103 aa）
Chain R 16–118（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.90 Å
7COW 353 bp di-nucleosome harboring cohesive DNA termini with linker histone H1.0 Deposited 2020-08-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CA CALCIUM ION × 3 K POTASSIUM ION × 5 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；potassium acetate, calcium chloride, potassium chloride
Resolution 2.86 Å R-free 0.297
7D1Z Cryo-EM structure of SET8-nucleosome complex Deposited 2020-09-15 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
7D20 Cryo-EM structure of SET8-CENP-A-nucleosome complex Deposited 2020-09-15 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7DBP Linker histone defines structure and self-association behaviour of the 177 bp human chromosome Deposited 2020-10-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7K5X Cryo-EM structure of a chromatosome containing human linker histone H1.0 Deposited 2020-09-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.93 Å
7K5Y Cryo-EM structure of a chromatosome containing human linker histone H1.4 Deposited 2020-09-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
7K60 Cryo-EM structure of a chromatosome containing human linker histone H1.10 Deposited 2020-09-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
7K61 Cryo-EM structure of 197bp nucleosome aided by scFv Deposited 2020-09-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.85 Å
7K63 Cryo-EM structure of a chromatosome containing chimeric linker histone gH1.10-ncH1.4 Deposited 2020-09-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
7LYA Cryo-EM structure of the human nucleosome core particle with linked histone proteins H2A and H2B Deposited 2021-03-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 13–130（118 aa）
Chain G 13–130（118 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.91 Å
7LYB Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c Deposited 2021-03-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 13–130（118 aa）
Chain G 13–130（118 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.28 Å
7LYC Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A Lys13 and Lys15 in complex with BARD1 (residues 415-777) Deposited 2021-03-06 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 13–130（118 aa）
Chain G 13–130（118 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
7NL0 Cryo-EM structure of the Lin28B nucleosome core particle Deposited 2021-02-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7PET The 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 34 PDB declaration: 36-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Chain m 1–130（130 aa）
Chain q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.50 Å
7PEU Trinucleosome of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
7PEV Nucleosome stack of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.00 Å
7PEW Nucleosome 1 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
7PEX Nucleosome 2 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
7PEY Nucleosome 3 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7PEZ Nucleosome 4 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain m 1–130（130 aa）
Chain q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.90 Å
7PF0 Trinucleosome of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.00 Å
7PF2 Nucleosome stack of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
7PF3 Nucleosome 4 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain m 1–130（130 aa）
Chain q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7PF4 Nucleosome 3 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7PF5 Nucleosome 2 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7PF6 Nucleosome 1 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7PFA Trinucleosome of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.70 Å
7PFC Nucleosome stack of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
7PFD Nucleosome 1 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7PFE Nucleosome 2 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7PFF Nucleosome 3 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7PFT Trinucleosome of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.80 Å
7PFU Nucleosome stack of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.00 Å
7PFV Nucleosome 1 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7PFW Nucleosome 2 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.20 Å
7PFX Nucleosome 3 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7V90 Telomeric mononucleosome Deposited 2021-08-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7V96 Telomeric Dinucleosome Deposited 2021-08-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.92 Å
7V99 catalytic core of human telomerase holoenzyme Deposited 2021-08-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: pentameric
Chain K 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7V9C Telomeric Dinucleosome in open state Deposited 2021-08-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7V9J Telomeric trinucleosome Deposited 2021-08-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain U 1–130（130 aa）
Chain Y 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.00 Å
7V9K Telomeric tetranucleosome Deposited 2021-08-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 34-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain U 1–130（130 aa）
Chain Y 1–130（130 aa）
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.10 Å
7V9S Telomeric trinucleosome in open state Deposited 2021-08-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain U 1–130（130 aa）
Chain Y 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.00 Å
7VA4 Telomeric tetranucleosome in open state Deposited 2021-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 34-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain U 1–130（130 aa）
Chain Y 1–130（130 aa）
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 14.00 Å
7VZ4 Cryo-EM structure of human nucleosome core particle composed of the Widom 601L DNA sequence Deposited 2021-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 1.89 Å
7W9V Cryo-EM structure of nucleosome in complex with p300 acetyltransferase catalytic core (complex I) Deposited 2021-12-10 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.95 Å
7WBV RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome Deposited 2021-12-17 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain c 2–130（129 aa）
Chain g 2–130（129 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7WBW RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3.5) of the nucleosome Deposited 2021-12-17 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain c 2–130（129 aa）
Chain g 2–130（129 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.10 Å
7WBX RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome Deposited 2021-12-17 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain c 2–130（129 aa）
Chain g 2–130（129 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7XD1 cryo-EM structure of unmodified nucleosome Deposited 2022-03-26 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 11–119（109 aa）
Chain G 11–119（109 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7XSE RNA polymerase II elongation complex transcribing a nucleosome (EC42) Deposited 2022-05-13 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7XSX RNA polymerase II elongation complex transcribing a nucleosome (EC49) Deposited 2022-05-15 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7XSZ RNA polymerase II elongation complex transcribing a nucleosome (EC115) Deposited 2022-05-15 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7XT7 RNA polymerase II elongation complex transcribing a nucleosome (EC49B) Deposited 2022-05-16 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7XTD RNA polymerase II elongation complex transcribing a nucleosome (EC58oct) Deposited 2022-05-16 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7XTI RNA polymerase II elongation complex transcribing a nucleosome (EC58hex) Deposited 2022-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7XVL Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an DNA fragment) Deposited 2022-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain W 1–130（130 aa）
Chain a 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 3.51 Å R-free 0.280
7XVL Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an DNA fragment) Deposited 2022-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain g 1–130（130 aa）
Chain k 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 3.51 Å R-free 0.280
7XVM Crystal Structure of Nucleosome-H5 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CA CALCIUM ION × 18 CL CHLORIDE ION × 3 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 2.84 Å R-free 0.259
7XX5 Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CA CALCIUM ION × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 3.19 Å R-free 0.259
7XX6 Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CA CALCIUM ION × 21 K POTASSIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 3.39 Å R-free 0.296
7XX6 Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric
Chain W 1–130（130 aa）
Chain a 1–130（130 aa）
Chain g 1–130（130 aa）
Chain k 1–130（130 aa）
Not recorded CA CALCIUM ION × 26 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 3.39 Å R-free 0.296
7XZX Cryo-EM structure of the nucleosome in complex with p53 DNA-binding domain Deposited 2022-06-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.53 Å
7XZY Cryo-EM structure of the nucleosome containing 193 base-pair DNA with a p53 target sequence Deposited 2022-06-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.97 Å
7XZZ Cryo-EM structure of the nucleosome in complex with p53 Deposited 2022-06-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.07 Å
7Y00 Cryo-EM structure of the nucleosome containing 169 base-pair DNA with a p53 target sequence Deposited 2022-06-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.96 Å
7Y7I chicken KNL2 in complex with the CENP-A nucleosome Deposited 2022-06-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Mutation：L51M, L58M, L93M Mutation：L51M, L58M, L93M No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.42 Å
7ZI4 Cryo-EM structure of the human INO80 complex bound to a WT nucleosome Deposited 2022-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain K 1–130（130 aa）
Chain O 1–130（130 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；4uL of sample applied to Quantifoil R2/2 Cu 300 mesh grids. blot parameters were wait time 30 sec, blot time 0.5 sec, blot force -8
Resolution 3.20 Å
8G57 Structure of nucleosome-bound Sirtuin 6 deacetylase Deposited 2023-02-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；12.5 mM HEPES pH 7.5, 60 mM KCl, 1.5% glycerol, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
8GRM Cryo-EM structure of PRC1 bound to H2AK119-UbcH5b-Ub nucleosome Deposited 2022-09-02 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 12–120（109 aa）
Chain G 12–120（109 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
8H0V RNA polymerase II transcribing a chromatosome (type I) Deposited 2022-09-30 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8H0W RNA polymerase II transcribing a chromatosome (type II) Deposited 2022-09-30 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8HAG Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 1 (3.2 angstrom resolution) Deposited 2022-10-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8HAH Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 2 (3.9 angstrom resolution) Deposited 2022-10-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8HAI Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 1 (4.7 angstrom resolution) Deposited 2022-10-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
8HAJ Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 2 (4.8 angstrom resolution) Deposited 2022-10-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
8HAK Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 4 (4.5 angstrom resolution) Deposited 2022-10-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
8HAL Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 1 Deposited 2022-10-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8HAM Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 2 Deposited 2022-10-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
8HAN Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 3 Deposited 2022-10-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
8HE5 RNA polymerase II elongation complex bound with Rad26 and Elf1, stalled at SHL(-3.5) of the nucleosome Deposited 2022-11-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 25-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.95 Å
8HQY Cryo-EM structure of SSX1 bound to the H2AK119Ub nucleosome at a resolution of 3.05 angstrom Deposited 2022-12-14 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 14–119（106 aa）
Chain G 14–119（106 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
8HR1 Cryo-EM structure of SSX1 bound to the unmodified nucleosome at a resolution of 3.02 angstrom Deposited 2022-12-14 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 14–119（106 aa）
Chain G 14–119（106 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.02 Å
8I17 Structural basis for H2A-H2B recognitions by human Spt16 Deposited 2023-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 14–113（100 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M MES monohydrate pH 6.0, 14% w/v Polyethylene glycol 4,000
Resolution 1.98 Å R-free 0.211
8I17 Structural basis for H2A-H2B recognitions by human Spt16 Deposited 2023-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 14–113（100 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M MES monohydrate pH 6.0, 14% w/v Polyethylene glycol 4,000
Resolution 1.98 Å R-free 0.211
8I17 Structural basis for H2A-H2B recognitions by human Spt16 Deposited 2023-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 14–113（100 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M MES monohydrate pH 6.0, 14% w/v Polyethylene glycol 4,000
Resolution 1.98 Å R-free 0.211
8IEG Bre1(mRBD-RING)/Rad6-Ub/nucleosome complex Deposited 2023-02-15 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 11–119（109 aa）
Chain G 11–119（109 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.44 Å
8IEJ RNF20-RNF40/hRad6A-Ub/nucleosome complex Deposited 2023-02-15 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 11–119（109 aa）
Chain G 11–119（109 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
8IHL Overlapping tri-nucleosome Deposited 2023-02-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain O 1–130（130 aa）
Chain S 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.64 Å
8JBX Human canonical 601 DNA nucleosome Deposited 2023-05-09 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
8JCC Human histone H2B variant H2BFWT Cryo-EM structure with 601 DNA sequence Deposited 2023-05-10 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.42 Å
8JCD Human H2BFWTH100R nucleosome with 601 DNA Deposited 2023-05-11 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.14 Å
8JH2 RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.70 Å
8JH3 RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8JH4 RNA polymerase II elongation complex containing 60 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8JHG Native SUV420H1 bound to 167-bp nucleosome Deposited 2023-05-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 16–130（115 aa）
Chain G 16–130（115 aa）
Not recorded ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane
Resolution 3.58 Å
8JL9 Cryo-EM structure of the human nucleosome with scFv Deposited 2023-06-02 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.65 Å
8JLA Cryo-EM structure of the human nucleosome lacking N-terminal region of H2A, H2B, H3, and H4 Deposited 2023-06-02 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 11–130（120 aa）
Chain G 11–130（120 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.44 Å
8JLB Cryo-EM structure of the 145 bp human nucleosome containing H3.2 C110A mutant Deposited 2023-06-02 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.36 Å
8JLD Cryo-EM structure of the 145 bp human nucleosome containing acetylated H3 tail Deposited 2023-06-02 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.48 Å
8JND The cryo-EM structure of the nonameric RAD51 ring bound to the nucleosome with the linker DNA binding Deposited 2023-06-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 19-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.66 Å
8JNE The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome without the linker DNA binding Deposited 2023-06-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.68 Å
8JNF The cryo-EM structure of the RAD51 filament bound to the nucleosome Deposited 2023-06-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.91 Å
8KB5 Cryo-EM structure of the human nucleosome containing H3.8 Deposited 2023-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.26 Å
8KCY Structure of nucleosome complexed with two DEK molecules Deposited 2023-08-08 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8KD1 Structure of nucleosome complexed with one DEK molecule Deposited 2023-08-08 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8KE0 Structure of H1.2 bound to the nucleosome Deposited 2023-08-11 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8OSJ Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL-6.2 (DNA conformation 1) Deposited 2023-04-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
8OSK Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL+5.8 (composite map) Deposited 2023-04-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8OSL Cryo-EM structure of CLOCK-BMAL1 bound to the native Por enhancer nucleosome (map 2, additional 3D classification and flexible refinement) Deposited 2023-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.90 Å
8OTS OCT4 and MYC-MAX co-bound to a nucleosome Deposited 2023-04-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded PTD PENTANEDIAL × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8OTT MYC-MAX bound to a nucleosome at SHL+5.8 Deposited 2023-04-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 9–117（109 aa）
Not recorded PTD PENTANEDIAL × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8Q36 Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Foamy Virus GAG Peptide-Au[I] Compound) Deposited 2023-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain CCC 14–120（107 aa）
Chain GGG 14–120（107 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0].
Resolution 2.60 Å R-free 0.262
8Q3E High Resolution Structure of Nucleosome Core with Bound Foamy Virus GAG Peptide Deposited 2023-08-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain CCC 14–120（107 aa）
Chain GGG 14–120（107 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
Resolution 2.17 Å R-free 0.270
8Q3M Structure of Nucleosome Core with a Bound Kaposi Sarcoma Associated Herpesvirus LANA Peptide Having a Methionine to Ornithine Substitution Deposited 2023-08-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain CCC 14–120（107 aa）
Chain GGG 14–120（107 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
Resolution 2.50 Å R-free 0.268
8Q3X Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Kaposi Sarcoma Associated Herpesvirus LANA Peptide-Au[I] Compound) Deposited 2023-08-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain CCC 14–120（107 aa）
Chain GGG 14–120（107 aa）
Not recorded AU GOLD ION × 1 XIS 4-diphenylphosphanylbenzoic acid × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
Resolution 2.30 Å R-free 0.262
8RGM Cryo-EM structure of nucleosome containing Widom603 DNA Deposited 2023-12-14 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8SMW Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 1) Deposited 2023-04-26 Different construct Different mutation/modification Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8SMX Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 2) Deposited 2023-04-26 Different construct Different mutation/modification Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SMY Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 3) Deposited 2023-04-26 Different construct Different mutation/modification Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SMZ Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (Class 4) Deposited 2023-04-26 Different construct Different mutation/modification Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SN0 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 5) Deposited 2023-04-26 Different construct Different mutation/modification Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SN1 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 6) Deposited 2023-04-26 Different construct Different mutation/modification Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8SN2 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c (UbcH5c chemically conjugated to histone H2A) Deposited 2023-04-26 Different construct Different mutation/modification Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8SN3 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8SN4 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN5 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 3) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8SN6 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 4) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN7 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 5) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN8 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 6) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN9 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8SNA Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8TXV Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 1) Deposited 2023-08-24 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：K13S Mutation：K13S No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8TXW Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 2) Deposited 2023-08-24 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：K13S Mutation：K13S No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8TXX Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 3) Deposited 2023-08-24 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：K13S Mutation：K13S No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8U13 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 1) Deposited 2023-08-30 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 13–130（118 aa）
Chain G 13–130（118 aa）
Mutation：K13S Mutation：K13S ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8U14 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 2) Deposited 2023-08-30 Different construct Different mutation/modification Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 13–130（118 aa）
Chain G 13–130（118 aa）
Mutation：K13S Mutation：K13S ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8U9S Cryo-EM structure of NRCAM nucleosome aided by scFv Deposited 2023-09-20 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8UBJ Cryo-EM structure of NRCAM nucleosome aided by scFv (3D Flex map) Deposited 2023-09-23 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8UBK Cryo-EM structure of Ascl1/E12a in complex with NRCAM nucleosome Deposited 2023-09-23 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8UBL Cryo-EM structure of Ascl1/E12a in complex with NRCAM nucleosome (3D Flex map) Deposited 2023-09-23 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8UPF Cryo-EM structure of the human nucleosome core particle in complex with RNF168-UbcH5c Deposited 2023-10-22 Different construct Different mutation/modification Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 13–130（118 aa）
Chain G 13–130（118 aa）
Mutation：R11S Mutation：R11S ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8UQ8 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 2-residue linker Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 13–106（94 aa）
Not recorded CL CHLORIDE ION × 7 GOL GLYCEROL × 3 ZN ZINC ION × 2 NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (9.5 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.34 Å R-free 0.236
8UQ8 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 2-residue linker Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain a 13–106（94 aa）
Not recorded CL CHLORIDE ION × 14 GOL GLYCEROL × 2 ZN ZINC ION × 2 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (9.5 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.34 Å R-free 0.236
8UQ9 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 4-residue linker Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 13–106（94 aa）
Not recorded CL CHLORIDE ION × 17 GOL GLYCEROL × 3 ZN ZINC ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (8.8 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.30 Å R-free 0.206
8UQ9 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 4-residue linker Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain a 13–106（94 aa）
Not recorded CL CHLORIDE ION × 19 GOL GLYCEROL × 3 ZN ZINC ION × 2 NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (8.8 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.30 Å R-free 0.206
8UQA Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 12-residue linker Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain K 13–106（94 aa）
Mutation：C85K in UbcH5c NA SODIUM ION × 3 ZN ZINC ION × 2 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (8.0 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.05 Å R-free 0.231
8UQB Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (crystallization condition 1) Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 13–106（94 aa）
Mutation：C85K in UbcH5c ZN ZINC ION × 2 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (12 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 50 mM BIS-TRIS propane, pH 7.0, 1 M NaCl
Resolution 2.48 Å R-free 0.260
8UQC Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (crystallization condition 2) Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 13–106（94 aa）
Mutation：C85K in UbcH5c ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (12 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 4% tacsimate, pH 6, 13.5% PEG3350
Resolution 2.61 Å R-free 0.252
8UQD Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (condition 2. RING not modeled in density) Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 13–106（94 aa）
Mutation：C85K in UbcH5c No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (12 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 4% tacsimate, pH 6, 13.5% PEG3350
Resolution 3.89 Å R-free 0.322
8UQE Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 26-residue linker (RING not modeled in density) Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 13–106（94 aa）
Mutation：S22R,C85K in UbcH5c No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (10 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M imidazole, pH 6.5, 1.0 M sodium acetate
Resolution 3.56 Å R-free 0.268
8VFX Cryo-EM structure of 186bp ALBN1 nucleosome aided by scFv Deposited 2023-12-22 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.65 Å
8VFY Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 1) Deposited 2023-12-22 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.89 Å
8VFZ Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 2) Deposited 2023-12-22 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8VG0 Cryo-EM structure of GATA4 in complex with ALBN1 nucleosome Deposited 2023-12-22 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
8VG1 Cryo-EM structure of FoxA1 and GATA4 in complex with ALBN1 nucleosome Deposited 2023-12-22 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.48 Å
8VG2 Cryo-EM structure of FoxA1 and GATA4 in complex with H14 chromatosome Deposited 2023-12-22 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
8VLR Cryo-EM structure of native H2AK119bu nucleosome at 2.6 Deposited 2024-01-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 12–119（108 aa）
Chain G 12–119（108 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Tris-HCl, pH 7.5, 50 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8W9D Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 1 Deposited 2023-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 7 K POTASSIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8W9E Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 2 Deposited 2023-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 7 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8W9F Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 3 Deposited 2023-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8WG5 Cryo-EM structure of USP16 bound to H2AK119Ub nucleosome Deposited 2023-09-20 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 11–119（109 aa）
Chain G 11–119（109 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
8X7I Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by intein-based E2-Ub-NCP conjugation strategy Deposited 2023-11-24 Different construct Different oligomeric state Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 11–121（111 aa）
Chain G 11–119（109 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
8X7J Cryo-EM structures of RNF168/UbcH5c-Ub/nucleosomes complex determined by activity-based chemical trapping strategy Deposited 2023-11-24 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 12–119（108 aa）
Chain G 11–118（108 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
8XBT The cryo-EM structure of the octameric RAD51 ring bound to the nucleosome with the linker DNA binding Deposited 2023-12-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.12 Å
8XBU The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome with the linker DNA binding Deposited 2023-12-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.24 Å
8XRJ RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei Deposited 2024-01-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain c 2–130（129 aa）
Chain g 2–130（129 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8XVS RNA polymerase II elongation complex with downstream nucleosome extracted from human nuclei Deposited 2024-01-15 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain c 2–130（129 aa）
Chain g 2–130（129 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8Y3C Cryo-EM structure of the overlapping di-nucleosome (closed form) Deposited 2024-01-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.21 Å
8Y3D Cryo-EM structure of the overlapping di-nucleosome (intermediate form2) Deposited 2024-01-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
8Y3E Cryo-EM structure of the overlapping di-nucleosome (open form) Deposited 2024-01-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.32 Å
8Y3F Cryo-EM structure of the overlapping di-nucleosome (intermediate form1) Deposited 2024-01-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.54 Å
8YBJ Cryo-EM structure of human nucleosome core particle composed of the Widom 601 DNA sequence Deposited 2024-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.38 Å
8YBK Cryo-EM structure of the human nucleosome containing the H3.1 E97K mutant Deposited 2024-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.69 Å
8YNY Structure of Cas9-sgRNA ribonucleoprotein bound to nucleosome Deposited 2024-03-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: 13-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.52 Å
8YTI Crystal Structure of Nucleosome-H1x Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2024-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CL CHLORIDE ION × 8 CA CALCIUM ION × 52 K POTASSIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45 mM CaCl2, 25 mM KCl, 10 mM Na-acetate (pH 4.5)
Resolution 2.70 Å R-free 0.267
8YV8 Cryo-EM structure of CDCA7 bound to nucleosome including hemimethylated CpG site in Widom601 positioning sequence. Deposited 2024-03-28 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8ZJR Structure of nucleosome-bound RFX5 complex Deposited 2024-05-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8ZJT Structure of free nucleosome Deposited 2024-05-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9BE5 Cryo-EM structure of Human Nucleosome collected by EPU on Glacios at 3.3 Angstrom resolution Deposited 2024-04-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain G 15–119（105 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9BE6 Cryo-EM structure of Human Nucleosome collected by Leginon on Krios at 3.0 Angstrom resolution Deposited 2024-04-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain G 15–119（105 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9GE5 CryoEM structure of the human INO80-Hexasome complex Deposited 2024-08-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain S 12–119（108 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
9GEL CryoEM structure of the human INO80-Hexasome complex Deposited 2024-08-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain S 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.86 Å
9GEV CryoEM structure of the human INO80 core-nucleosome complex state N-6 Deposited 2024-08-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain O 2–130（129 aa）
Chain S 2–130（129 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
9GF6 CryoEM structure of the human INO80 core-nucleosome complex state N-6 Deposited 2024-08-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain O 2–130（129 aa）
Chain S 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9GFB CryoEM structure of the human INO80 core-nucleosome complex state N-7 Deposited 2024-08-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain O 2–130（129 aa）
Chain S 2–130（129 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 6 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
9GFM CryoEM structure of the human INO80 core-nucleosome complex state N-7 Deposited 2024-08-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain O 14–119（106 aa）
Chain S 9–119（111 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9GW2 State 2 MAP 1 SETD2 bound to proximal H3 of upstream nucleosome Deposited 2024-09-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.84 Å
9IGW Ku70/80 bound to 147 bp nucleosome Deposited 2025-02-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å
9IGX Ku70/80 bound to 153 bp nucleosome Deposited 2025-02-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain C 12–121（110 aa）
Chain G 12–121（110 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.56 Å
9IPU cryo-EM structure of the RNF168(1-193)/UbcH5c-Ub ubiquitylation module bound to H1.0-K63-Ub3 modified chromatosome Deposited 2024-07-11 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
9J0N Paused elongation complex of mammalian RNA polymerase II with nucleosome (PEC2-nuc) Deposited 2024-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 27 PDB declaration: 30-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9J0O Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC1-nuc) Deposited 2024-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9J0P Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC2-nuc) Deposited 2024-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9J8M Cryo-EM structure of BAF-Lamin A/C IgF-nucleosome complex (High mobility complex) Deposited 2024-08-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.82 Å
9J8N Cryo-EM structure of BAF-Lamin A/C IgF-nucleosome complex (Low mobility complex) Deposited 2024-08-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 32-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.14 Å
9J8O Cryo-EM structure of BAF-Lamin A/C IgF-H1-nucleosome complex Deposited 2024-08-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 28-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.05 Å
9J8W Cryo-EM structure of NCP-UV-DDB complex containing CPD Deposited 2024-08-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.38 Å
9JC6 Human H2BW2 nucleosome Deposited 2024-08-28 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.34 Å
9KQO cryo-EM structure of RNF20/RNF40-RAD6A-Ub in complex with H2BS112GlcNAc nucleosome Deposited 2024-11-26 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded ZN ZINC ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.48 Å
9L1X hDEK-nucleosome complex (conformation 1) Deposited 2024-12-16 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 2–120（119 aa）
Chain G 2–120（119 aa）
Not recorded UNX UNKNOWN LIGAND × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.69 Å
9L22 hDEK-nucleosome complex (conformation 2) Deposited 2024-12-16 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded UNX UNKNOWN LIGAND × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9R04 p53 bound to the nucleosome at position SHL-5.7 (crosslinked sample) Deposited 2025-04-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9R2M p53 bound to nucleosome at position SHL+5.9 (non-crosslinked sample, composite map) Deposited 2025-04-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9R2P p53 bound to nucleosome at position SHL+5.9 (crosslinked sample) Deposited 2025-04-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.18 Å
9R2Q p53 bound to nucleosome at position SHL-5.7 (non-crosslinked sample) Deposited 2025-04-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9RL4 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL-6 Deposited 2025-06-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded PTD PENTANEDIAL × 16 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9RMC Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 1 Deposited 2025-06-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9RN1 Structure of BAF-nucleosome complex with OCT4-SOX2 at SHL+6 in ADP-bound state, BAF47 bound to ATPase lobe 2 Deposited 2025-06-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.90 Å
9RN2 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 2 Deposited 2025-06-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 19 PDB declaration: 21-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
9RZC State 3 MAP 1 SETD2 bound to distal H3 of upstream nucleosome Deposited 2025-07-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.66 Å
9RZE State 2 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to proximal upstream H3 Deposited 2025-07-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.53 Å
9S0U State 3 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to distal upstream H3 Deposited 2025-07-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.72 Å
9S3G State 1 MAP3 RNA Pol II activated elongation complex with SETD2 and upstream hexasome Deposited 2025-07-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
9U5U The 1:1 cryo-EM structure of BAP1/ASXL1-K351Ub in complex with H2AK119Ub nucleosome Deposited 2025-03-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
9UZ7 Cryo-EM structure of the nucleosome core particle with site-specific DNA-histone crosslinking Deposited 2025-05-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain E 2–130（129 aa）
Chain F 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；10 mM HEPES, pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution not provided
9WMS Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type B) Deposited 2025-09-03 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9WMT Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type A) Deposited 2025-09-03 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
9WMU Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type A) Deposited 2025-09-03 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.28 Å
9WMV Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type B) Deposited 2025-09-03 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.66 Å
9WMW Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, FACT-hexamer) Deposited 2025-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
9XSF Cryo-EM structure of H4S47GlcNAc nucleosome at 3.39 angstrom Deposited 2025-11-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.39 Å
9YL3 State 1 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.50 Å
9YLE State 3 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.63 Å
9YLY MLL4FC bound to a nucleosome with p53 RE Deposited 2025-10-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 14 PDB declaration: 16-meric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.77 Å
9YM8 State 2 focused on PHD FYR of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.43 Å
9YMF State 2 focused on H3 N terminal tail of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.45 Å
9ZEN Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1B2 Deposited 2025-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain C 11–121（111 aa）
Chain G 11–121（111 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES pH7.6, 50 mM NaCl, 0.5 mM MgCl2, 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.17 Å
9ZEO Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1G1 Deposited 2025-11-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 11–121（111 aa）
Chain G 11–121（111 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES pH7.6, 50 mM NaCl, 0.5 mM MgCl2, 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å

343 other PDB entries and 350 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H2A1B_HUMAN
Isoform —
PDB entities 3, 5
Chains and sequence ranges Author chain C； PDBConstruct 1–105； UniProt 15–119 Author chain G； PDBConstruct 1–108； UniProt 11–118

Histone H2B type 1-K

Homo sapiens

UniProt O60814

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 10 DNA 2 PDB declaration: dodecameric（12） Consistent with all polymer counts Chain D； UniProt 32–125 Chain H； UniProt 32–125 Not recorded Histone H3.2 × 2 （Q71DI3） Histone H4 × 2 （P62805） Histone H2A type 1-B/E × 1 （P04908） Histone H2A type 1-B/E × 1 （P04908） DNA (143-MER) × 1 DNA (143-MER) × 1 Ubiquitin-conjugating enzyme E2 D3 × 1 （P61077） E3 ubiquitin-protein ligase RNF168 × 1 （Q8IYW5） ZN ZINC ION × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.27 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8X7K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2CV5 Crystal structure of human nucleosome core particle Deposited 2005-05-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 0–125（126 aa）
Chain H 0–125（126 aa）
Not recorded MN MANGANESE (II) ION × 9 CL CHLORIDE ION × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.277
6KE9 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-07-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 32–126（95 aa）
Chain H 32–126（95 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
Resolution 2.22 Å R-free 0.230
6L9H The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-11-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 32–126（95 aa）
Chain H 32–126（95 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
Resolution 2.60 Å R-free 0.278
6LE9 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-11-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 32–126（95 aa）
Chain H 32–126（95 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
Resolution 2.60 Å R-free 0.281
6T79 Structure of a human nucleosome at 3.2 A resolution Deposited 2019-10-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 3.20 Å
6T7A Structure of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 3.70 Å
6T7B Structure of human Sox2 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 5.10 Å
6T7C Structure of two copies of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 4.00 Å
6T7D Structure of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 4.40 Å
6V92 RSC-NCP Deposited 2019-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 33 PDB declaration: 35-meric
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 20.00 Å
6Y5D Structure of human cGAS (K394E) bound to the nucleosome Deposited 2020-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain P 1–126（126 aa）
Chain T 1–126（126 aa）
Not recorded PTD PENTANEDIAL × 9 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6Y5E Structure of human cGAS (K394E) bound to the nucleosome (focused refinement of cGAS-NCP subcomplex) Deposited 2020-02-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 33–125（93 aa）
Chain H 32–125（94 aa）
Not recorded PTD PENTANEDIAL × 8 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
7BWD Structure of Dot1L-H2BK34ub Nucleosome Complex Deposited 2020-04-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.32 Å
7DBP Linker histone defines structure and self-association behaviour of the 177 bp human chromosome Deposited 2020-10-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7JZV Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome Deposited 2020-09-02 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain O 2–126（125 aa）
Chain o 2–126（125 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7PET The 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 34 PDB declaration: 36-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Chain n 1–126（126 aa）
Chain r 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.50 Å
7PEU Trinucleosome of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
7PEV Nucleosome stack of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.00 Å
7PEW Nucleosome 1 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
7PEX Nucleosome 2 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
7PEY Nucleosome 3 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7PEZ Nucleosome 4 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain e 1–126（126 aa）
Chain n 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.90 Å
7PF0 Trinucleosome of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.00 Å
7PF2 Nucleosome stack of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
7PF3 Nucleosome 4 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain n 1–126（126 aa）
Chain r 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7PF4 Nucleosome 3 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7PF5 Nucleosome 2 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7PF6 Nucleosome 1 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7PFA Trinucleosome of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.70 Å
7PFC Nucleosome stack of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
7PFD Nucleosome 1 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7PFE Nucleosome 2 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7PFF Nucleosome 3 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7PFT Trinucleosome of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.80 Å
7PFU Nucleosome stack of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.00 Å
7PFV Nucleosome 1 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7PFW Nucleosome 2 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.20 Å
7PFX Nucleosome 3 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7V90 Telomeric mononucleosome Deposited 2021-08-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 28–126（99 aa）
Chain H 28–126（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7V96 Telomeric Dinucleosome Deposited 2021-08-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain D 28–126（99 aa）
Chain H 28–126（99 aa）
Chain N 28–126（99 aa）
Chain R 28–126（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.92 Å
7V99 catalytic core of human telomerase holoenzyme Deposited 2021-08-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: pentameric
Chain L 2–126（125 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7V9C Telomeric Dinucleosome in open state Deposited 2021-08-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain D 32–126（95 aa）
Chain H 32–126（95 aa）
Chain N 32–126（95 aa）
Chain R 32–126（95 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7V9J Telomeric trinucleosome Deposited 2021-08-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain D 28–126（99 aa）
Chain H 28–126（99 aa）
Chain N 28–126（99 aa）
Chain R 28–126（99 aa）
Chain V 28–126（99 aa）
Chain Z 28–126（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.00 Å
7V9K Telomeric tetranucleosome Deposited 2021-08-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 34-meric
Chain D 28–126（99 aa）
Chain H 28–126（99 aa）
Chain N 28–126（99 aa）
Chain R 28–126（99 aa）
Chain V 28–126（99 aa）
Chain Z 28–126（99 aa）
Chain d 28–126（99 aa）
Chain h 28–126（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.10 Å
7V9S Telomeric trinucleosome in open state Deposited 2021-08-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain D 28–126（99 aa）
Chain H 28–126（99 aa）
Chain N 28–126（99 aa）
Chain R 28–126（99 aa）
Chain V 28–126（99 aa）
Chain Z 28–126（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.00 Å
7VA4 Telomeric tetranucleosome in open state Deposited 2021-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 34-meric
Chain D 32–126（95 aa）
Chain H 32–126（95 aa）
Chain N 32–126（95 aa）
Chain R 32–126（95 aa）
Chain V 32–126（95 aa）
Chain Z 32–126（95 aa）
Chain d 32–126（95 aa）
Chain h 32–126（95 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 14.00 Å
7XCR Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 1:1 complex Deposited 2022-03-25 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 32–125（94 aa）
Chain H 32–125（94 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.57 Å
7XCT Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 2:1 complex Deposited 2022-03-25 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 33–125（93 aa）
Chain H 33–125（93 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
7XD1 cryo-EM structure of unmodified nucleosome Deposited 2022-03-26 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 32–125（94 aa）
Chain H 32–125（94 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8GRM Cryo-EM structure of PRC1 bound to H2AK119-UbcH5b-Ub nucleosome Deposited 2022-09-02 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 31–126（96 aa）
Chain H 32–126（95 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
8HQY Cryo-EM structure of SSX1 bound to the H2AK119Ub nucleosome at a resolution of 3.05 angstrom Deposited 2022-12-14 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 35–125（91 aa）
Chain H 35–125（91 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
8HR1 Cryo-EM structure of SSX1 bound to the unmodified nucleosome at a resolution of 3.02 angstrom Deposited 2022-12-14 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain D 35–125（91 aa）
Chain H 35–125（91 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.02 Å
8IEG Bre1(mRBD-RING)/Rad6-Ub/nucleosome complex Deposited 2023-02-15 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain D 32–125（94 aa）
Chain H 32–125（94 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.44 Å
8IEJ RNF20-RNF40/hRad6A-Ub/nucleosome complex Deposited 2023-02-15 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain D 32–125（94 aa）
Chain H 32–125（94 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
8JHF Native SUV420H1 bound to 167-bp nucleosome Deposited 2023-05-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 32–126（95 aa）
Chain H 32–126（95 aa）
Not recorded ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane
Resolution 3.68 Å
8JHG Native SUV420H1 bound to 167-bp nucleosome Deposited 2023-05-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 32–126（95 aa）
Chain H 32–126（95 aa）
Not recorded ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane
Resolution 3.58 Å
8Q36 Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Foamy Virus GAG Peptide-Au[I] Compound) Deposited 2023-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain DDD 32–126（95 aa）
Chain HHH 32–126（95 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0].
Resolution 2.60 Å R-free 0.262
8Q3E High Resolution Structure of Nucleosome Core with Bound Foamy Virus GAG Peptide Deposited 2023-08-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain DDD 32–126（95 aa）
Chain HHH 32–126（95 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
Resolution 2.17 Å R-free 0.270
8Q3M Structure of Nucleosome Core with a Bound Kaposi Sarcoma Associated Herpesvirus LANA Peptide Having a Methionine to Ornithine Substitution Deposited 2023-08-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain DDD 32–126（95 aa）
Chain HHH 32–126（95 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
Resolution 2.50 Å R-free 0.268
8Q3X Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Kaposi Sarcoma Associated Herpesvirus LANA Peptide-Au[I] Compound) Deposited 2023-08-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain DDD 32–126（95 aa）
Chain HHH 32–126（95 aa）
Not recorded AU GOLD ION × 1 XIS 4-diphenylphosphanylbenzoic acid × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
Resolution 2.30 Å R-free 0.262
8W9D Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 1 Deposited 2023-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded ZN ZINC ION × 7 K POTASSIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8W9E Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 2 Deposited 2023-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded ZN ZINC ION × 7 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8W9F Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 3 Deposited 2023-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8WG5 Cryo-EM structure of USP16 bound to H2AK119Ub nucleosome Deposited 2023-09-20 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 32–125（94 aa）
Chain H 32–125（94 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
8X7I Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by intein-based E2-Ub-NCP conjugation strategy Deposited 2023-11-24 Different oligomeric state Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain D 32–125（94 aa）
Chain H 32–125（94 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
8X7J Cryo-EM structures of RNF168/UbcH5c-Ub/nucleosomes complex determined by activity-based chemical trapping strategy Deposited 2023-11-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain D 32–125（94 aa）
Chain H 32–125（94 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
8YV8 Cryo-EM structure of CDCA7 bound to nucleosome including hemimethylated CpG site in Widom601 positioning sequence. Deposited 2024-03-28 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8ZJR Structure of nucleosome-bound RFX5 complex Deposited 2024-05-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8ZJT Structure of free nucleosome Deposited 2024-05-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9D3R 147-bp 5S rDNA nucleosome - closed Deposited 2024-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 30–125（96 aa）
Chain H 30–125（96 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9ECP Structure of the native human NCP purified from HEK293 cells Deposited 2024-11-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 32–125（94 aa）
Chain H 32–125（94 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.91 Å
9GW2 State 2 MAP 1 SETD2 bound to proximal H3 of upstream nucleosome Deposited 2024-09-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.84 Å
9IPU cryo-EM structure of the RNF168(1-193)/UbcH5c-Ub ubiquitylation module bound to H1.0-K63-Ub3 modified chromatosome Deposited 2024-07-11 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
9KQO cryo-EM structure of RNF20/RNF40-RAD6A-Ub in complex with H2BS112GlcNAc nucleosome Deposited 2024-11-26 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded ZN ZINC ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.48 Å
9RZC State 3 MAP 1 SETD2 bound to distal H3 of upstream nucleosome Deposited 2025-07-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.66 Å
9RZE State 2 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to proximal upstream H3 Deposited 2025-07-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.53 Å
9S0U State 3 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to distal upstream H3 Deposited 2025-07-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.72 Å
9S3G State 1 MAP3 RNA Pol II activated elongation complex with SETD2 and upstream hexasome Deposited 2025-07-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain h 1–126（126 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
9U5U The 1:1 cryo-EM structure of BAP1/ASXL1-K351Ub in complex with H2AK119Ub nucleosome Deposited 2025-03-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
9XSF Cryo-EM structure of H4S47GlcNAc nucleosome at 3.39 angstrom Deposited 2025-11-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.39 Å
9ZEN Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1B2 Deposited 2025-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain D 34–126（93 aa）
Chain H 34–126（93 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES pH7.6, 50 mM NaCl, 0.5 mM MgCl2, 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.17 Å
9ZEO Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1G1 Deposited 2025-11-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain D 32–126（95 aa）
Chain H 32–126（95 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES pH7.6, 50 mM NaCl, 0.5 mM MgCl2, 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å

82 other PDB entries and 82 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H2B1K_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D； PDBConstruct 1–94； UniProt 32–125 Author chain H； PDBConstruct 1–94； UniProt 32–125

Ubiquitin-conjugating enzyme E2 D3

Homo sapiens

UniProt P61077

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 10 DNA 2 PDB declaration: dodecameric（12） Consistent with all polymer counts Chain K； UniProt 1–147 Not recorded Histone H3.2 × 2 （Q71DI3） Histone H4 × 2 （P62805） Histone H2A type 1-B/E × 1 （P04908） Histone H2B type 1-K × 2 （O60814） Histone H2A type 1-B/E × 1 （P04908） DNA (143-MER) × 1 DNA (143-MER) × 1 E3 ubiquitin-protein ligase RNF168 × 1 （Q8IYW5） ZN ZINC ION × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.27 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8X7K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1X23 Crystal structure of ubch5c Deposited 2005-04-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–147（147 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；0.1M HEPES-Na, 10% iso-propanol, 20% PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 1.85 Å R-free 0.282
1X23 Crystal structure of ubch5c Deposited 2005-04-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–147（147 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；0.1M HEPES-Na, 10% iso-propanol, 20% PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 1.85 Å R-free 0.282
1X23 Crystal structure of ubch5c Deposited 2005-04-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–147（147 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；0.1M HEPES-Na, 10% iso-propanol, 20% PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 1.85 Å R-free 0.282
1X23 Crystal structure of ubch5c Deposited 2005-04-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–147（147 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；0.1M HEPES-Na, 10% iso-propanol, 20% PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 1.85 Å R-free 0.282
2FUH Solution Structure of the UbcH5c/Ub Non-covalent Complex Deposited 2006-01-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–147（146 aa） Fragment：UbcH5c
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 150mM NaCl；Pressure ambient
NMR sample composition 1mM UbcH5c U-15N,13C 25mM sodium phosphate 150mM NaCl | 90% H20 10% D20
NMR sample composition 1mM Ubiquitin U-15N,13C 25mM sodium phosphate 150mM NaCl | 90% H20 10% D20
NMR sample composition 1mM UbcH5c U-15N,13C 1mM Ubiquitin 25mM sodium phosphate 150mM NaCl | 90% H20 10% D20
NMR sample composition 1mM Ubiquitin U-15N,13C 1mM UbcH5c 25mM sodium phosphate 150mM NaCl | 90% H20 10% D20
NMR sample composition 1mM UbcH5c U-15N,13C 1mM Ubiquitin 25mM sodium phosphate 150mM NaCl | 100% D20
NMR sample composition 1mM Ubiquitin U-15N,13C 1mM UbcH5c 25mM sodium phosphate 150mM NaCl | 100% D20
Resolution not provided
3L1Z Crystal structure of the U-BOX domain of human E4B ubiquitin ligase in complex with UBCH5C E2 ubiquitin conjugating enzyme Deposited 2009-12-14 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–147（147 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；4M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 3.17 Å R-free 0.279
3L1Z Crystal structure of the U-BOX domain of human E4B ubiquitin ligase in complex with UBCH5C E2 ubiquitin conjugating enzyme Deposited 2009-12-14 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–147（147 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；4M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 3.17 Å R-free 0.279
3RPG Bmi1/Ring1b-UbcH5c complex structure Deposited 2011-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–147（146 aa）
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；40% MPD, 0.1 M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.65 Å R-free 0.243
3RPG Bmi1/Ring1b-UbcH5c complex structure Deposited 2011-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–147（146 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；40% MPD, 0.1 M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.65 Å R-free 0.243
3UGB UbcH5c~Ubiquitin Conjugate Deposited 2011-11-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–147（147 aa） Fragment：unp residues 1-147
Mutation：C85S GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.2M tri-potassium citrate, 20% PEG 3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.35 Å R-free 0.252
4BVU Structure of Shigella effector OspG in complex with host UbcH5c- Ubiquitin conjugate Deposited 2013-06-28 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–147（147 aa）
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.1 M TRIS PH 8.5, 20% ETOH
Resolution 2.70 Å R-free 0.291
4R8P Crystal structure of the Ring1B/Bmi1/UbcH5c PRC1 ubiquitylation module bound to the nucleosome core particle Deposited 2014-09-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain L 2–147（146 aa） Fragment：Residues 2-116 of Ring1B and Residues 2-148 of UbcH5c
Chain N 2–147（146 aa） Fragment：Residues 2-116 of Ring1B and Residues 2-148 of UbcH5c
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions Modified micro batch under oil；pH 7.5；294 K；25 mM HEPES pH 7.5, 80 mM NH4NO3, 3 % PEG2000-MME, Modified micro batch under oil, temperature 294K
Resolution 3.28 Å R-free 0.245
4S3O PCGF5-RING1B-UbcH5c complex Deposited 2015-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 2–147（146 aa）
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；277 K；13.5% PEG 550 MME, 10 mM TCEP, 0.1 M MES pH 6.5, 100 mM KCl, VAPOR DIFFUSION, temperature 277K
Resolution 2.00 Å R-free 0.237
4S3O PCGF5-RING1B-UbcH5c complex Deposited 2015-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–147（146 aa）
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；277 K；13.5% PEG 550 MME, 10 mM TCEP, 0.1 M MES pH 6.5, 100 mM KCl, VAPOR DIFFUSION, temperature 277K
Resolution 2.00 Å R-free 0.237
5EGG Crystal structure of human ubiquitin-conjugating enzyme UBCH5C Deposited 2015-10-27 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–147（147 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；2% v/v Tacsimate pH 4.0, 0.1 M Sodium acetate trihydrate pH 4.6, 16% w/v Polyethylene glycol 3350
Resolution 1.76 Å R-free 0.253
5IFR Structure of the stable UBE2D3-UbDha conjugate Deposited 2016-02-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–147（146 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；200mM tripotassium citrate, 20% PEG 3350
Resolution 2.20 Å R-free 0.243
6CP0 SdcA in complex with the E2, UbcH5C Deposited 2018-03-13 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–147（147 aa）
Mutation：C85S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；1.5 M ammonium sulfate, 3% glycerol, 0.1 M HEPES pH 7.5
Resolution 3.01 Å R-free 0.261
6T7F RCR E3 ligase E2-Ubiquitin transthiolation intermediate Deposited 2019-10-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–147（146 aa）
Mutation：C21S, S22R, C107S, C111S ZN ZINC ION × 6 LWZ 3,3-bis(sulfanyl)-~{N}-(1~{H}-1,2,3-triazol-4-ylmethyl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；0.85 M sodium citrate, 100 mM sodium chloride, 100 mM Tris-HCl pH 8.0
Resolution 2.58 Å R-free 0.256
7JZV Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome Deposited 2020-09-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 2–147（146 aa）
Mutation：UbcH5c C85K ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7LYB Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c Deposited 2021-03-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain P 2–147（146 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.28 Å
8AMS Complex of human TRIM2 RING domain, UBCH5C, and Ubiquitin Deposited 2022-08-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–147（147 aa）
Chain B 1–147（147 aa）
Not recorded GOL GLYCEROL × 9 ZN ZINC ION × 4 PE8 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.2 M sodium formate, 0.1 M bis-tris propane, 20% PEG 3350
Resolution 2.40 Å R-free 0.233
8SMW Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 1) Deposited 2023-04-26 Different mutation/modification Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain L 1–147（147 aa）
Mutation：C21I, C107A, C111D, L119K ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8SMX Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 2) Deposited 2023-04-26 Different mutation/modification Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain L 1–147（147 aa）
Mutation：C21I, C107A, C111D, L119K ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SMY Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 3) Deposited 2023-04-26 Different mutation/modification Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain L 1–147（147 aa）
Mutation：C21I, C107A, C111D, L119K ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SMZ Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (Class 4) Deposited 2023-04-26 Different mutation/modification Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain L 1–147（147 aa）
Mutation：C21I, C107A, C111D, L119K ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SN0 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 5) Deposited 2023-04-26 Different mutation/modification Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain L 1–147（147 aa）
Mutation：C21I, C107A, C111D, L119K ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SN1 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 6) Deposited 2023-04-26 Different mutation/modification Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain L 1–147（147 aa）
Mutation：C21I, C107A, C111D, L119K ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8SN2 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c (UbcH5c chemically conjugated to histone H2A) Deposited 2023-04-26 Different mutation/modification Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain L 1–147（147 aa）
Mutation：C21I, C107A, C111D, L119K ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8SN3 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain L 1–147（147 aa）
Mutation：C21I, C107A, C111D, L119K ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8SN4 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain L 1–147（147 aa）
Mutation：C21I, C107A, C111D, L119K ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN5 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 3) Deposited 2023-04-26 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain L 1–147（147 aa）
Mutation：C21I, C107A, C111D, L119K ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8SN6 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 4) Deposited 2023-04-26 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain L 1–147（147 aa）
Mutation：C21I, C107A, C111D, L119K ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN7 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 5) Deposited 2023-04-26 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain L 1–147（147 aa）
Mutation：C21I, C107A, C111D, L119K ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN8 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 6) Deposited 2023-04-26 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain L 1–147（147 aa）
Mutation：C21I, C107A, C111D, L119K ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN9 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain L 1–147（147 aa）
Mutation：C21I, C107A, C111D, L119K ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8SNA Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain L 1–147（147 aa）
Mutation：C21I, C107A, C111D, L119K ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8U14 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 2) Deposited 2023-08-30 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain L 2–147（146 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8UPF Cryo-EM structure of the human nucleosome core particle in complex with RNF168-UbcH5c Deposited 2023-10-22 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain L 2–147（146 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8UQ8 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 2-residue linker Deposited 2023-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–147（146 aa）
Not recorded CL CHLORIDE ION × 7 GOL GLYCEROL × 3 ZN ZINC ION × 2 NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (9.5 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.34 Å R-free 0.236
8UQ8 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 2-residue linker Deposited 2023-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain a 2–147（146 aa）
Not recorded CL CHLORIDE ION × 14 GOL GLYCEROL × 2 ZN ZINC ION × 2 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (9.5 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.34 Å R-free 0.236
8UQ9 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 4-residue linker Deposited 2023-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–147（146 aa）
Not recorded CL CHLORIDE ION × 17 GOL GLYCEROL × 3 ZN ZINC ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (8.8 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.30 Å R-free 0.206
8UQ9 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 4-residue linker Deposited 2023-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain a 2–147（146 aa）
Not recorded CL CHLORIDE ION × 19 GOL GLYCEROL × 3 ZN ZINC ION × 2 NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (8.8 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.30 Å R-free 0.206
8UQA Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 12-residue linker Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain K 2–147（146 aa）
Mutation：C85K in UbcH5c NA SODIUM ION × 3 ZN ZINC ION × 2 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (8.0 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.05 Å R-free 0.231
8UQB Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (crystallization condition 1) Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–147（146 aa）
Mutation：C85K in UbcH5c ZN ZINC ION × 2 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (12 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 50 mM BIS-TRIS propane, pH 7.0, 1 M NaCl
Resolution 2.48 Å R-free 0.260
8UQC Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (crystallization condition 2) Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–147（146 aa）
Mutation：C85K in UbcH5c ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (12 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 4% tacsimate, pH 6, 13.5% PEG3350
Resolution 2.61 Å R-free 0.252
8UQD Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (condition 2. RING not modeled in density) Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–147（146 aa）
Mutation：C85K in UbcH5c No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (12 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 4% tacsimate, pH 6, 13.5% PEG3350
Resolution 3.89 Å R-free 0.322
8UQE Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 26-residue linker (RING not modeled in density) Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–147（146 aa）
Mutation：S22R,C85K in UbcH5c No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (10 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M imidazole, pH 6.5, 1.0 M sodium acetate
Resolution 3.56 Å R-free 0.268
8X7I Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by intein-based E2-Ub-NCP conjugation strategy Deposited 2023-11-24 Different oligomeric state Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain K 1–147（147 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
8X7J Cryo-EM structures of RNF168/UbcH5c-Ub/nucleosomes complex determined by activity-based chemical trapping strategy Deposited 2023-11-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain K 1–147（147 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
9IPU cryo-EM structure of the RNF168(1-193)/UbcH5c-Ub ubiquitylation module bound to H1.0-K63-Ub3 modified chromatosome Deposited 2024-07-11 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain K 1–147（147 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
9LPK Structure of human PADI6-UHRF1-UBE2D3 complex Deposited 2025-01-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain D 1–147（147 aa）
Chain E 1–147（147 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen OTHER
Resolution 3.03 Å
9V9Q Cryo-EM structure of the cPRC1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome Deposited 2025-06-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain P 1–147（147 aa）
Mutation：C85S, S22R No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.80 Å
9V9R Cryo-EM structure of the ncPRC1.1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome Deposited 2025-06-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain P 1–147（147 aa）
Mutation：C85S, S22R No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.20 Å

45 other PDB entries and 53 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UB2D3_HUMAN
Isoform —
PDB entities 8
Chains and sequence ranges Author chain K； PDBConstruct 1–147； UniProt 1–147

E3 ubiquitin-protein ligase RNF168

Homo sapiens

UniProt Q8IYW5

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 10 DNA 2 PDB declaration: dodecameric（12） Consistent with all polymer counts Chain L； UniProt 1–113 Not recorded Histone H3.2 × 2 （Q71DI3） Histone H4 × 2 （P62805） Histone H2A type 1-B/E × 1 （P04908） Histone H2B type 1-K × 2 （O60814） Histone H2A type 1-B/E × 1 （P04908） DNA (143-MER) × 1 DNA (143-MER) × 1 Ubiquitin-conjugating enzyme E2 D3 × 1 （P61077） ZN ZINC ION × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.27 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8X7K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3L11 Crystal Structure of the Ring Domain of RNF168 Deposited 2009-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–113（113 aa） Fragment：ring domain (UNP residues 1-113)
Not recorded ZN ZINC ION × 2 MLI MALONATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；291 K；1.5 M NaMalonate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.12 Å R-free 0.215
4GB0 Crystal Structure of the RING domain of RNF168 Deposited 2012-07-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–111（111 aa） Fragment：UNP residues 1-111
Not recorded MLI MALONATE ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1.6M sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.60 Å R-free 0.276
5XIS Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form I Deposited 2017-04-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 110–188（79 aa） Fragment：UNP residues 110-188
Not recorded XYZ beta-D-xylofuranose × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；15% PEG3350, 0.1 M Tris-HCl (pH 8.5), 100 mM MgCl2
Resolution 1.78 Å R-free 0.245
5XIS Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form I Deposited 2017-04-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 110–188（79 aa） Fragment：UNP residues 110-188
Not recorded XYZ beta-D-xylofuranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；15% PEG3350, 0.1 M Tris-HCl (pH 8.5), 100 mM MgCl2
Resolution 1.78 Å R-free 0.245
5XIT Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form II Deposited 2017-04-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 113–188（76 aa） Fragment：UNP residues 113-188
Not recorded GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；23% PEG MME 2000, 0.1 M Bis-Tris (pH 6.5), 10 mM Pr acetate
Resolution 2.25 Å R-free 0.239
5XIT Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form II Deposited 2017-04-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 113–188（76 aa） Fragment：UNP residues 113-188
Not recorded GOL GLYCEROL × 1 PR PRASEODYMIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；23% PEG MME 2000, 0.1 M Bis-Tris (pH 6.5), 10 mM Pr acetate
Resolution 2.25 Å R-free 0.239
5XIU Crystal structure of RNF168 UDM2 in complex with Lys63-linked diubiquitin Deposited 2017-04-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 419–462（44 aa） Fragment：UNP residues 419-462
Not recorded EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；25% PEG3350, 0.1 M Tris-HCl (pH8.5), 0.2 M Ammonium Acetate
Resolution 1.80 Å R-free 0.207
5YDK Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, tetrameric form Deposited 2017-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 113–194（82 aa） Fragment：UNP residues 113-194
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH 7.6 21% PEG3350
Resolution 2.50 Å R-free 0.260
5YDK Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, tetrameric form Deposited 2017-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 113–194（82 aa） Fragment：UNP residues 113-194
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH 7.6 21% PEG3350
Resolution 2.50 Å R-free 0.260
5YDK Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, tetrameric form Deposited 2017-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 113–194（82 aa） Fragment：UNP residues 113-194
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH 7.6 21% PEG3350
Resolution 2.50 Å R-free 0.260
5YDK Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, tetrameric form Deposited 2017-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain L 113–194（82 aa） Fragment：UNP residues 113-194
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH 7.6 21% PEG3350
Resolution 2.50 Å R-free 0.260
8SMW Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 1) Deposited 2023-04-26 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 1–93（93 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8SMX Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 2) Deposited 2023-04-26 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 1–93（93 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SMY Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 3) Deposited 2023-04-26 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 1–93（93 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SMZ Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (Class 4) Deposited 2023-04-26 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 1–93（93 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SN0 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 5) Deposited 2023-04-26 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 1–93（93 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SN1 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 6) Deposited 2023-04-26 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 1–93（93 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8SN2 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c (UbcH5c chemically conjugated to histone H2A) Deposited 2023-04-26 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 1–93（93 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8SN3 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain K 1–93（93 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8SN4 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain K 1–93（93 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN5 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 3) Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain K 1–93（93 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8SN6 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 4) Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain K 1–93（93 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN7 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 5) Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain K 1–93（93 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN8 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 6) Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain K 1–93（93 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN9 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain K 1–93（93 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8SNA Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain K 1–93（93 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8TXV Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 1) Deposited 2023-08-24 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 1–571（571 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8TXW Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 2) Deposited 2023-08-24 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 1–571（571 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8TXX Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 3) Deposited 2023-08-24 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 1–571（571 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8U13 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 1) Deposited 2023-08-30 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain K 1–94（94 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8U14 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 2) Deposited 2023-08-30 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 1–94（94 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8UPF Cryo-EM structure of the human nucleosome core particle in complex with RNF168-UbcH5c Deposited 2023-10-22 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 1–94（94 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8UQ8 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 2-residue linker Deposited 2023-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–94（94 aa）
Not recorded CL CHLORIDE ION × 7 GOL GLYCEROL × 3 ZN ZINC ION × 2 NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (9.5 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.34 Å R-free 0.236
8UQ8 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 2-residue linker Deposited 2023-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain a 1–94（94 aa）
Not recorded CL CHLORIDE ION × 14 GOL GLYCEROL × 2 ZN ZINC ION × 2 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (9.5 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.34 Å R-free 0.236
8UQ9 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 4-residue linker Deposited 2023-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–94（94 aa）
Not recorded CL CHLORIDE ION × 17 GOL GLYCEROL × 3 ZN ZINC ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (8.8 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.30 Å R-free 0.206
8UQ9 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 4-residue linker Deposited 2023-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain a 1–94（94 aa）
Not recorded CL CHLORIDE ION × 19 GOL GLYCEROL × 3 ZN ZINC ION × 2 NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (8.8 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.30 Å R-free 0.206
8UQA Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 12-residue linker Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain K 1–94（94 aa）
Mutation：C85K in UbcH5c NA SODIUM ION × 3 ZN ZINC ION × 2 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (8.0 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.05 Å R-free 0.231
8UQB Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (crystallization condition 1) Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–94（94 aa）
Mutation：C85K in UbcH5c ZN ZINC ION × 2 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (12 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 50 mM BIS-TRIS propane, pH 7.0, 1 M NaCl
Resolution 2.48 Å R-free 0.260
8UQC Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (crystallization condition 2) Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–94（94 aa）
Mutation：C85K in UbcH5c ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (12 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 4% tacsimate, pH 6, 13.5% PEG3350
Resolution 2.61 Å R-free 0.252
8UQD Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (condition 2. RING not modeled in density) Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–94（94 aa）
Mutation：C85K in UbcH5c No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (12 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 4% tacsimate, pH 6, 13.5% PEG3350
Resolution 3.89 Å R-free 0.322
8UQE Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 26-residue linker (RING not modeled in density) Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–94（94 aa）
Mutation：S22R,C85K in UbcH5c No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (10 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M imidazole, pH 6.5, 1.0 M sodium acetate
Resolution 3.56 Å R-free 0.268
8X7I Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by intein-based E2-Ub-NCP conjugation strategy Deposited 2023-11-24 Different oligomeric state Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain L 1–113（113 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
8X7J Cryo-EM structures of RNF168/UbcH5c-Ub/nucleosomes complex determined by activity-based chemical trapping strategy Deposited 2023-11-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain L 1–113（113 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
9IPU cryo-EM structure of the RNF168(1-193)/UbcH5c-Ub ubiquitylation module bound to H1.0-K63-Ub3 modified chromatosome Deposited 2024-07-11 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain L 1–193（193 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
9KQ2 Cryo-EM structure of RNF168'-RNF168-UbcH5c complex bound to nucleosome Deposited 2024-11-25 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain K 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å

38 other PDB entries and 45 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RN168_HUMAN
Isoform —
PDB entities 9
Chains and sequence ranges Author chain L； PDBConstruct 1–113； UniProt 1–113

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 8x7k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8x7k
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8x7k
Deposition date deposition_date2023-11-24
Structure title titleCryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination)
Keywords keywordsRNF168, nucleosome, H2AK13/15 ubiquitination, NUCLEAR PROTEIN, NUCLEAR PROTEIN-DNA complex; NUCLEAR PROTEIN/DNA
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier41.57 Å
Radius of gyration Rg (electron density) rg_electron39.52 Å
Forward intensity I(0) i0968027000.00
Molecular weight molecular_weight195680.0 kDa
Excluded volume excluded_volume220010 ų
Envelope volume envelope_volume328380 ų
Hydration-shell volume shell_volume68077 ų
Envelope diameter envelope_diameter136.8 Å
Shell Rg shell_rg46.36 Å
Envelope Rg envelope_rg38.73 Å
Shape Rg shape_rg39.41 Å
Total Rg total_rg40.08 Å
Total atoms total_atoms13387
Residues n_residues1240
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax126.9 Å
Rg (real space) rg_real41.34 Å
Rg uncertainty (real space) rg_real_error0.88 Å
I(0) (real space) i0_real9.6800e+08
I(0) uncertainty (real space) i0_real_error1.7980e+07
Rg (reciprocal space) rg_reciprocal41.57 Å
I(0) (reciprocal space) i0_reciprocal968300000.0000
Solution quality estimate total_estimate0.9029
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary50.1 Å
Skewness Skewness skewness0.050
Kurtosis Kurtosis kurtosis-0.612
Angular range angular_range— – 0.1900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha58450000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.940; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.944
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (10)

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8. Citations (1)

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9. Files and Curves (10)