Histone H3.2
Homo sapiens
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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count | Chain A； UniProt 57–136 | Fragment：UNP residues 57-136 | Histone H4 × 1 （P62805） DNA replication licensing factor MCM2 × 1 （P49736） Histone chaperone ASF1B × 1 （Q9NVP2） 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 |
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 5BO0 | 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 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
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 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: 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 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: 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 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: 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 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: 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 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 × 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 mutation/modification 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: 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 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 × 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 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 × 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 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 × 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 oligomeric state Different ligand/ion 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 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 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 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 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 |
| 5VAC Crystal Structure of ATXR5 SET domain in complex with K36me3 histone H3 peptide Deposited 2017-03-24 | Different construct Different oligomeric state Different ligand/ion 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 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 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 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）
|
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 mutation/modification 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 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 mutation/modification 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification 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 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 mutation/modification 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 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 mutation/modification 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 method 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 mutation/modification 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 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 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 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 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 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 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 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 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 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 mutation/modification 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 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 mutation/modification 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 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 experimental method Different experimental conditions 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 method 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 method 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 method 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 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）
|
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 mutation/modification 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 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 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 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 mutation/modification 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 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 method 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 method 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 mutation/modification 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 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 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 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 mutation/modification 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 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 mutation/modification 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 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 method 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 method 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 mutation/modification 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 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 mutation/modification 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 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 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 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 method 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 method 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 mutation/modification 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 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 mutation/modification 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 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 mutation/modification 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification 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 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 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
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 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
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 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
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 method 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 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 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 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 experimental method 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）
|
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 experimental method 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）
|
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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 method 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 method 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 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 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 method 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 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
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 mutation/modification 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: 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 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
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 mutation/modification 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: 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | 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 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 × 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 |
| 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) Deposited 2023-11-24 | 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 × 10 PDB declaration: dodecameric |
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 3.27 Å |
| 8ZJR Structure of nucleosome-bound RFX5 complex Deposited 2024-05-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–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 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）
|
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 experimental method Different experimental conditions 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 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
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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 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
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 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
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 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
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 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
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 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
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 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
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 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
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 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: 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 mutation/modification 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: 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 mutation/modification 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: 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 mutation/modification 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: 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 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: 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 mutation/modification 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: 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 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: 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 mutation/modification 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: 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 method 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 method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 method 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 method 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 method 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 method 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 method 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 method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 method 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 mutation/modification 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: 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 mutation/modification 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 mutation/modification 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: 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 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）
|
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 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）
|
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 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）
|
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 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）
|
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 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）
|
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 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）
|
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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 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
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 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
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 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 × 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 1–80； UniProt 57–136 |
