Histone H3.1
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–DNA Heteromer Protein × 24 DNA 2 PDB declaration: 26-meric（26） Consistent with all polymer counts | Chain A； UniProt 1–136 Chain E； UniProt 1–136 Chain K； UniProt 1–136 Chain O； UniProt 1–136 Chain S； UniProt 1–136 Chain W； UniProt 1–136 | Not recorded | Histone H4 × 6 （P62805） Histone H2A type 1-B/E × 6 （P04908） Histone H2B type 1-K × 6 （O60814） DNA (408-mer) × 1 DNA (408-mer) × 1 | ELECTRON MICROSCOPY cryo-EM buffer：pH 6 cryo-EM vitrification conditions：Cryogen ETHANE | Resolution 8.00 Å |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 7V9J | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 2B2T Tandem chromodomains of human CHD1 complexed with Histone H3 Tail containing trimethyllysine 4 and phosphothreonine 3 Deposited 2005-09-19 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain D
1–19（19 aa）
Fragment：residues 1-19
|
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；283 K；4% PEG3350, 0.05M HEPES, pH 8.0, 10mM BTP, 12.5mM NaCl, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 283K, pH 8.00
|
Resolution 2.45 Å R-free 0.266 |
| 2B2U Tandem chromodomains of human CHD1 complexed with Histone H3 Tail containing trimethyllysine 4 and dimethylarginine 2 Deposited 2005-09-19 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain D
1–15（15 aa）
Fragment：residues 1-15
|
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；283 K；4% PEG3350, 0.05M HEPES, pH 8.0, 10mM BTP, 12.5mM NaCl, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 283K, pH 8.00
|
Resolution 2.95 Å R-free 0.290 |
| 2B2V Crystal structure analysis of human CHD1 chromodomains 1 and 2 bound to histone H3 resi 1-15 MeK4 Deposited 2005-09-19 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain D
1–15（15 aa）
Fragment：residues 1-15
|
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；283 K；4% PEG3350, 0.05M HEPES, pH 8.0, 10mM BTP, 12.5mM NaCl, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 283K, pH 8.00
|
Resolution 2.65 Å R-free 0.266 |
| 2B2W Tandem chromodomains of human CHD1 complexed with Histone H3 Tail containing trimethyllysine 4 Deposited 2005-09-19 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain D
1–19（19 aa）
Fragment：residues 1-19
|
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；283 K；4% PEG3350, 0.05M HEPES pH 8.0, 10mM BTP, 12.5mM NaCl, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 283K, pH 8.00
|
Resolution 2.40 Å R-free 0.273 |
| 2CV5 Crystal structure of human nucleosome core particle Deposited 2005-05-31 | 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 × 8 PDB declaration: decameric |
Chain A
0–135（136 aa）
Chain E
0–135（136 aa）
|
Not recorded | MN MANGANESE (II) ION × 9 CL CHLORIDE ION × 4 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.50 Å R-free 0.277 |
| 2L75 Solution structure of CHD4-PHD2 in complex with H3K9me3 Deposited 2010-12-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–14（13 aa）
Fragment：UNP residues 2-14
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
SOLUTION NMR
NMR measurement conditions
pH 7；298 K；Ionic strength (raw mmCIF value) 15；Pressure ambient
NMR sample composition
1 mM CHD4-PHD2-1; 1 mM H3K9me3-2, 20 uM DSS-3; 1 mM DTT-4; 5 mM sodium chloride-5; 10 mM sodium phosphate-6; 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition
1 mM [U-100% 13C; U-100% 15N] CHD4-PHD2-7; 1.1 mM H3K9me3-8; 20 uM DSS-9; 1 mM DTT-10; 5 mM sodium chloride-11; 10 mM sodium phosphate-12; 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition
1 mM [U-100% 13C; U-100% 15N] CHD4-PHD2-13; 1.1 mM H3K9me3-14; 20 uM DSS-15; 1 mM DTT-16; 5 mM sodium chloride-17; 10 mM sodium phosphate-18; 100% D2O | 100% D2O
|
Resolution not provided |
| 2RI7 Crystal structure of PHD finger-linker-bromodomain Y17E mutant from human BPTF in the H3(1-9)K4ME2 bound state Deposited 2007-10-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain P
2–10（9 aa）
Fragment：N-terminal tail residues 2-10
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 GOL GLYCEROL × 1 IPA ISOPROPYL ALCOHOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；BPTF Y17E PHD finger-linker-bromodomain (16.5 mg/ml, 20 mM Tris-HCl pH 7.5, 50 mM KCl) was pre-incubated with three-fold molar excess of H3(1-9)K4me2 peptide in the presence of 5 mM MgCl2 for about 30 min on ice. Drops were made by mixing 2 l each of the complex with the reservoir solution: 8.5% isopropanol, 0.085 M Hepes-Na, pH 7.5, 17% PEG 4000, 15% Glycerol. A 0.3 l of 1 M KCl was then added to the drops as additive., VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.45 Å R-free 0.192 |
| 2UXN Structural Basis of Histone Demethylation by LSD1 Revealed by Suicide Inactivation Deposited 2007-03-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
2–22（21 aa）
Fragment：HISTONE H3-DERIVED SUICIDE INHIBITOR, RESIDUES 2-22
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | FDA DIHYDROFLAVINE-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.6；PROTEIN: 25 MM HEPES, PH 7.4, 200 MM SODIUM CHLORIDE, 1 MM PMSF, AND 5 MM DTT RESERVOIR: 0.8 M LITHIUM SULFATE, 0.8 M AMMONIUM SULFATE, 0.4 M SODIUM CHLORIDE, 0.1 M SODIUM CITRATE, PH 5.6, AND 10 MM DTT
|
Resolution 2.72 Å R-free 0.272 |
| 3A1B Crystal structure of the DNMT3A ADD domain in complex with histone H3 Deposited 2009-03-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–21（20 aa）
Fragment：ADD(ATRX-DNMT3-DNMT3L) domain(residues 476-614), UNP residues 2-21(Histone H3.1)
|
Not recorded | ZN ZINC ION × 3 EDO 1,2-ETHANEDIOL × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；10% PEG 2000 monomethyl ether, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.29 Å R-free 0.224 |
| 3AFA The human nucleosome structure Deposited 2010-02-24 | 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 × 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 × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.50 Å R-free 0.270 |
| 3AYW Crystal Structure of Human Nucleosome Core Particle Containing H3K56Q mutation Deposited 2011-05-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：K56Q Mutation：K56Q | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 2.90 Å R-free 0.273 |
| 3AZE Crystal Structure of Human Nucleosome Core Particle Containing H3K64Q mutation Deposited 2011-05-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：K64Q Mutation：K64Q | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 10 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 3.00 Å R-free 0.302 |
| 3AZF Crystal Structure of Human Nucleosome Core Particle Containing H3K79Q mutation Deposited 2011-05-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：K79Q Mutation：K79Q | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 2.70 Å R-free 0.263 |
| 3AZG Crystal Structure of Human Nucleosome Core Particle Containing H3K115Q mutation Deposited 2011-05-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：K115Q Mutation：K115Q | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 9 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 2.40 Å R-free 0.269 |
| 3AZH Crystal Structure of Human Nucleosome Core Particle Containing H3K122Q mutation Deposited 2011-05-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：K122Q Mutation：K122Q | CL CHLORIDE ION × 3 MN MANGANESE (II) ION × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 3.49 Å R-free 0.266 |
| 3AZI Crystal Structure of Human Nucleosome Core Particle Containing H4K31Q mutation Deposited 2011-05-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 13 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 2.70 Å R-free 0.289 |
| 3AZJ Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q mutation Deposited 2011-05-25 | Different construct Different 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 | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 2.89 Å R-free 0.268 |
| 3AZK Crystal Structure of Human Nucleosome Core Particle Containing H4K59Q mutation Deposited 2011-05-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 3.20 Å R-free 0.258 |
| 3AZL Crystal Structure of Human Nucleosome Core Particle Containing H4K77Q mutation Deposited 2011-05-25 | Different construct Different 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 | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 2.70 Å R-free 0.259 |
| 3AZM Crystal Structure of Human Nucleosome Core Particle Containing H4K79Q mutation Deposited 2011-05-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | CL CHLORIDE ION × 3 MN MANGANESE (II) ION × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 2.89 Å R-free 0.296 |
| 3AZN Crystal Structure of Human Nucleosome Core Particle Containing H4K91Q mutation Deposited 2011-05-25 | Different construct Different 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 | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 3.00 Å R-free 0.254 |
| 3KMT Crystal structure of vSET/SAH/H3 ternary complex Deposited 2009-11-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
26–33（8 aa）
Fragment：residues 26-33
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；293 K；26% PEG 4000, 0.1 M sodium citrate pH 6.3, 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.78 Å R-free 0.224 |
| 3KMT Crystal structure of vSET/SAH/H3 ternary complex Deposited 2009-11-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain H
26–33（8 aa）
Fragment：residues 26-33
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；293 K；26% PEG 4000, 0.1 M sodium citrate pH 6.3, 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.78 Å R-free 0.224 |
| 3KMT Crystal structure of vSET/SAH/H3 ternary complex Deposited 2009-11-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain I
26–33（8 aa）
Fragment：residues 26-33
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；293 K；26% PEG 4000, 0.1 M sodium citrate pH 6.3, 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.78 Å R-free 0.224 |
| 3KMT Crystal structure of vSET/SAH/H3 ternary complex Deposited 2009-11-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain G
26–33（8 aa）
Fragment：residues 26-33
Chain H
26–33（8 aa）
Fragment：residues 26-33
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；293 K；26% PEG 4000, 0.1 M sodium citrate pH 6.3, 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.78 Å R-free 0.224 |
| 3KMT Crystal structure of vSET/SAH/H3 ternary complex Deposited 2009-11-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain I
26–33（8 aa）
Fragment：residues 26-33
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；293 K；26% PEG 4000, 0.1 M sodium citrate pH 6.3, 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.78 Å R-free 0.224 |
| 3KQI crystal structure of PHF2 PHD domain complexed with H3K4Me3 peptide Deposited 2009-11-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–12（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；2.0 M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.78 Å R-free 0.218 |
| 3KQI crystal structure of PHF2 PHD domain complexed with H3K4Me3 peptide Deposited 2009-11-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–12（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 4 GOL GLYCEROL × 2 CL CHLORIDE ION × 2 MG MAGNESIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；2.0 M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.78 Å R-free 0.218 |
| 3LQI Crystal structure of MLL1 PHD3-Bromo complexed with H3(1-9)K4me2 peptide Deposited 2010-02-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain R
2–10（9 aa）
Fragment：Histone H3 N-terminal tail
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；293 K；0.1 M Bis-Tris, 0.2 M ammonium acetate, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.92 Å R-free 0.241 |
| 3LQI Crystal structure of MLL1 PHD3-Bromo complexed with H3(1-9)K4me2 peptide Deposited 2010-02-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain S
2–10（9 aa）
Fragment：Histone H3 N-terminal tail
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；293 K；0.1 M Bis-Tris, 0.2 M ammonium acetate, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.92 Å R-free 0.241 |
| 3LQI Crystal structure of MLL1 PHD3-Bromo complexed with H3(1-9)K4me2 peptide Deposited 2010-02-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain T
2–10（9 aa）
Fragment：Histone H3 N-terminal tail
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；293 K；0.1 M Bis-Tris, 0.2 M ammonium acetate, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.92 Å R-free 0.241 |
| 3LQJ Crystal structure of MLL1 PHD3-Bromo complexed with H3(1-9)K4me3 peptide Deposited 2010-02-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain Q
2–10（9 aa）
Fragment：Histone H3 N-terminal tail
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；293 K；0.1 M Tris, 0.2 M Li2SO4, 15% PEG3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.90 Å R-free 0.274 |
| 3LQJ Crystal structure of MLL1 PHD3-Bromo complexed with H3(1-9)K4me3 peptide Deposited 2010-02-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain T
2–10（9 aa）
Fragment：Histone H3 N-terminal tail
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；293 K；0.1 M Tris, 0.2 M Li2SO4, 15% PEG3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.90 Å R-free 0.274 |
| 3O34 Crystal structure of TRIM24 PHD-Bromo complexed with H3(13-32)K23ac peptide Deposited 2010-07-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
14–33（20 aa）
Fragment：UNP residues 14-35
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 BTN BIOTIN × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；100 mM Na-citrate (pH 5.6), 200 mM K/Na-tartrate tetrahydrate and 1.6 M ammonium sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.90 Å R-free 0.241 |
| 3O35 Crystal structure of TRIM24 PHD-Bromo complexed with H3(23-31)K27ac peptide Deposited 2010-07-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
24–32（9 aa）
Fragment：UNP residues 14 -22
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；200 mM Na-acetate, 30% Polyethylene glycol 4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.76 Å R-free 0.225 |
| 3O35 Crystal structure of TRIM24 PHD-Bromo complexed with H3(23-31)K27ac peptide Deposited 2010-07-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
24–32（9 aa）
Fragment：UNP residues 14 -22
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；200 mM Na-acetate, 30% Polyethylene glycol 4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.76 Å R-free 0.225 |
| 3O37 Crystal structure of TRIM24 PHD-Bromo complexed with H3(1-10)K4 peptide Deposited 2010-07-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
2–11（10 aa）
Fragment：UNP residues 2-11
|
Not recorded | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；50 mM Tris (pH 7.5), 30% Polyethylene glycol monomethyl ether 5000 and 100 mM NaCl , VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.00 Å R-free 0.254 |
| 3O37 Crystal structure of TRIM24 PHD-Bromo complexed with H3(1-10)K4 peptide Deposited 2010-07-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
2–11（10 aa）
Fragment：UNP residues 2-11
|
Not recorded | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；50 mM Tris (pH 7.5), 30% Polyethylene glycol monomethyl ether 5000 and 100 mM NaCl , VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.00 Å R-free 0.254 |
| 3O37 Crystal structure of TRIM24 PHD-Bromo complexed with H3(1-10)K4 peptide Deposited 2010-07-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
2–11（10 aa）
Fragment：UNP residues 2-11
|
Not recorded | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；50 mM Tris (pH 7.5), 30% Polyethylene glycol monomethyl ether 5000 and 100 mM NaCl , VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.00 Å R-free 0.254 |
| 3O37 Crystal structure of TRIM24 PHD-Bromo complexed with H3(1-10)K4 peptide Deposited 2010-07-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain H
2–11（10 aa）
Fragment：UNP residues 2-11
|
Not recorded | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；50 mM Tris (pH 7.5), 30% Polyethylene glycol monomethyl ether 5000 and 100 mM NaCl , VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.00 Å R-free 0.254 |
| 3U4S Histone Lysine demethylase JMJD2A in complex with T11C peptide substrate crosslinked to N-oxalyl-D-cysteine Deposited 2011-10-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
8–15（8 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 08P N-(carboxycarbonyl)-D-cysteine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；20% PEG 3350, 0.1M citrate, 2 mM NiCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.15 Å R-free 0.222 |
| 3U4S Histone Lysine demethylase JMJD2A in complex with T11C peptide substrate crosslinked to N-oxalyl-D-cysteine Deposited 2011-10-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
8–15（8 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 08P N-(carboxycarbonyl)-D-cysteine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；20% PEG 3350, 0.1M citrate, 2 mM NiCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.15 Å R-free 0.222 |
| 3U5N Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-20)K9me3K14ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
2–21（20 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9 and acetylated K14, UNP residues 2-21
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M ammonium tartrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.95 Å R-free 0.256 |
| 3U5N Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-20)K9me3K14ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
2–21（20 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9 and acetylated K14, UNP residues 2-21
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M ammonium tartrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.95 Å R-free 0.256 |
| 3U5O Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain I
2–23（22 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14 and K18, UNP residues 2-23
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M sodium citrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.70 Å R-free 0.280 |
| 3U5O Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain J
2–23（22 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14 and K18, UNP residues 2-23
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M sodium citrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.70 Å R-free 0.280 |
| 3U5O Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain K
2–23（22 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14 and K18, UNP residues 2-23
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M sodium citrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.70 Å R-free 0.280 |
| 3U5O Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain L
2–23（22 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14 and K18, UNP residues 2-23
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M sodium citrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.70 Å R-free 0.280 |
| 3U5O Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain M
2–23（22 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14 and K18, UNP residues 2-23
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M sodium citrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.70 Å R-free 0.280 |
| 3U5O Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain N
2–23（22 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14 and K18, UNP residues 2-23
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M sodium citrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.70 Å R-free 0.280 |
| 3U5O Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain O
2–23（22 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14 and K18, UNP residues 2-23
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M sodium citrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.70 Å R-free 0.280 |
| 3U5O Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain P
2–23（22 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14 and K18, UNP residues 2-23
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M sodium citrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.70 Å R-free 0.280 |
| 3U5P Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-28)K9me3K14acK18acK23ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain I
2–29（28 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14, K18 and K23, UNP residues 2-29
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M lithium sulfate, 0.1 mM Tris pH 8.0 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.80 Å R-free 0.265 |
| 3U5P Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-28)K9me3K14acK18acK23ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain J
2–29（28 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14, K18 and K23, UNP residues 2-29
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M lithium sulfate, 0.1 mM Tris pH 8.0 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.80 Å R-free 0.265 |
| 3U5P Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-28)K9me3K14acK18acK23ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain K
2–29（28 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14, K18 and K23, UNP residues 2-29
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M lithium sulfate, 0.1 mM Tris pH 8.0 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.80 Å R-free 0.265 |
| 3U5P Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-28)K9me3K14acK18acK23ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain L
2–29（28 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14, K18 and K23, UNP residues 2-29
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M lithium sulfate, 0.1 mM Tris pH 8.0 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.80 Å R-free 0.265 |
| 3U5P Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-28)K9me3K14acK18acK23ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain M
2–29（28 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14, K18 and K23, UNP residues 2-29
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M lithium sulfate, 0.1 mM Tris pH 8.0 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.80 Å R-free 0.265 |
| 3U5P Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-28)K9me3K14acK18acK23ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain N
2–29（28 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14, K18 and K23, UNP residues 2-29
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M lithium sulfate, 0.1 mM Tris pH 8.0 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.80 Å R-free 0.265 |
| 3U5P Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-28)K9me3K14acK18acK23ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain O
2–29（28 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14, K18 and K23, UNP residues 2-29
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M lithium sulfate, 0.1 mM Tris pH 8.0 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.80 Å R-free 0.265 |
| 3U5P Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-28)K9me3K14acK18acK23ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain P
2–29（28 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14, K18 and K23, UNP residues 2-29
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M lithium sulfate, 0.1 mM Tris pH 8.0 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.80 Å R-free 0.265 |
| 3V43 Crystal structure of MOZ Deposited 2011-12-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain Q
2–19（18 aa）
Fragment：UNP RESIDUES 2-19
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 4 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；0.2M ammonium acetate, 0.1M tri-sodium citrate, 30% w/v PEG 4000, pH 5.6, vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.47 Å R-free 0.176 |
| 3W96 Crystal Structure of Human Nucleosome Core Particle lacking H2A N-terminal region Deposited 2013-04-01 | 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 | CL CHLORIDE ION × 1 MN MANGANESE (II) ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 3.00 Å R-free 0.296 |
| 3W97 Crystal Structure of Human Nucleosome Core Particle lacking H2B N-terminal region Deposited 2013-04-01 | Different construct Different 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 | MN MANGANESE (II) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 3.20 Å R-free 0.321 |
| 3W98 Crystal Structure of Human Nucleosome Core Particle lacking H3.1 N-terminal region Deposited 2013-04-01 | Different construct Different 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
29–136（108 aa）
Fragment：UNP residues 29-136
Chain E
29–136（108 aa）
Fragment：UNP residues 29-136
|
Not recorded | MN MANGANESE (II) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 3.42 Å R-free 0.303 |
| 3W99 Crystal Structure of Human Nucleosome Core Particle lacking H4 N-terminal region Deposited 2013-04-01 | Different construct Different 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 | MN MANGANESE (II) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 3.00 Å R-free 0.312 |
| 3WA9 The nucleosome containing human H2A.Z.1 Deposited 2013-04-30 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 3.07 Å R-free 0.271 |
| 3WAA The nucleosome containing human H2A.Z.2 Deposited 2013-04-30 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 3.20 Å R-free 0.271 |
| 3WKJ The nucleosome containing human TSH2B Deposited 2013-10-22 | 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 × 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 × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.80 Å R-free 0.291 |
| 3X1S Crystal structure of the nucleosome core particle Deposited 2014-11-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | MN MANGANESE (II) ION × 6 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；60-70mM KCL, 70-90mM MnCl2, 24% MPD, 20mM Na-Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.81 Å R-free 0.270 |
| 3X1T Crystal structure of nucleosome core particle consisting of mouse testis specific histone variants H2aa and H2ba Deposited 2014-11-27 | Different construct Different 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 | MN MANGANESE (II) ION × 22 CL CHLORIDE ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；60-70mM Kcl, 70-90mM MnCl2, 24% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.81 Å R-free 0.266 |
| 3X1U Crystal structure of nucleosome core particle in the presence of histone variants involved in reprogramming Deposited 2014-11-28 | Different construct Different 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 | MN MANGANESE (II) ION × 4 CL CHLORIDE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；60-70 mM KCl, 70-90 mM MnCl2, 24% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.25 Å R-free 0.270 |
| 3X1V Crystal structure of nucleosome core particle in the presence of histone variant involved in reprogramming Deposited 2014-11-28 | Different construct Different 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 | MN MANGANESE (II) ION × 19 CL CHLORIDE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；60-70 mM KCl, 70-90 mM MnCl2, Na-cocodylate, 24% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.92 Å R-free 0.259 |
| 3ZVY PHD finger of human UHRF1 in complex with unmodified histone H3 N- terminal tail Deposited 2011-07-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
2–9（8 aa）
Fragment：RESIDUES 2-9
|
Not recorded | ZN ZINC ION × 4 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；290 K；CRYSTALS WERE OBTAINED AT 17 DEGREES USING THE VAPOR DIFFUSION METHOD BY MIXING A PROTEIN SOLUTION AT A CONCENTRATION OF 606 MICROM (IN 20 MM TRIS PH 7, 150 MM NACL, 0.5 MM TCEP, 25 MICROM ZNCL2 AND 0.1 MM PMSF) AND 10-FOLD EXCESS OF PEPTIDE WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION (0.1 M TRIS PH 8.5, 0.2 M MGCL2, 30 % PEG 4000). CRYSTALS WERE CRYOPROTECTED WITH 15 % MPD AND FLASH FROZEN IN LIQUID NITROGEN.
|
Resolution 1.95 Å R-free 0.227 |
| 3ZVY PHD finger of human UHRF1 in complex with unmodified histone H3 N- terminal tail Deposited 2011-07-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
2–9（8 aa）
Fragment：RESIDUES 2-9
|
Not recorded | ZN ZINC ION × 4 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；290 K；CRYSTALS WERE OBTAINED AT 17 DEGREES USING THE VAPOR DIFFUSION METHOD BY MIXING A PROTEIN SOLUTION AT A CONCENTRATION OF 606 MICROM (IN 20 MM TRIS PH 7, 150 MM NACL, 0.5 MM TCEP, 25 MICROM ZNCL2 AND 0.1 MM PMSF) AND 10-FOLD EXCESS OF PEPTIDE WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION (0.1 M TRIS PH 8.5, 0.2 M MGCL2, 30 % PEG 4000). CRYSTALS WERE CRYOPROTECTED WITH 15 % MPD AND FLASH FROZEN IN LIQUID NITROGEN.
|
Resolution 1.95 Å R-free 0.227 |
| 4BD3 Phf19 links methylated lysine 36 of histone H3 to regulation of Polycomb activity Deposited 2012-10-04 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
32–42（11 aa）
Fragment：H3(31-41)K36ME3, RESIDUES 32-42
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7；298 K；Ionic strength (raw mmCIF value) 200；Pressure 1.0
NMR sample composition
90% WATER/10% D2O
|
Resolution not provided |
| 4C1Q Crystal structure of the PRDM9 SET domain in complex with H3K4me2 and AdoHcy. Deposited 2013-08-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
2–11（10 aa）
Fragment：N-TERMINUS, RESIDUES 2-11
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.5；278 K；0.2 M AMMONIUM SULFATE, 0.1 M BIS-TRIS PH 5.5 AND 25% W/V PEG3350
|
Resolution 2.30 Å R-free 0.252 |
| 4F4U The bicyclic intermediate structure provides insights into the desuccinylation mechanism of SIRT5 Deposited 2012-05-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
5–16（12 aa）
Fragment：UNP residue 5-16
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；16% PEG 4000, 6% Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.261 |
| 4F4U The bicyclic intermediate structure provides insights into the desuccinylation mechanism of SIRT5 Deposited 2012-05-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
5–16（12 aa）
Fragment：UNP residue 5-16
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；16% PEG 4000, 6% Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.261 |
| 4F56 The bicyclic intermediate structure provides insights into the desuccinylation mechanism of SIRT5 Deposited 2012-05-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
5–16（12 aa）
Fragment：UNP residue 5-16
|
Not recorded | ZN ZINC ION × 1 CGK 3-[(2R,3aR,5R,6R,6aR)-5-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-2,6-dihydroxytetrahydrofuro[2,3-d][1,3]oxathiol-2-yl]propanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30% PEG 10000, 0.1M Tris, pH 8.5, vapor diffusion, hanging drop, temperature 298K
|
Resolution 1.70 Å R-free 0.233 |
| 4F56 The bicyclic intermediate structure provides insights into the desuccinylation mechanism of SIRT5 Deposited 2012-05-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
5–16（12 aa）
Fragment：UNP residue 5-16
|
Not recorded | ZN ZINC ION × 1 CGK 3-[(2R,3aR,5R,6R,6aR)-5-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-2,6-dihydroxytetrahydrofuro[2,3-d][1,3]oxathiol-2-yl]propanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30% PEG 10000, 0.1M Tris, pH 8.5, vapor diffusion, hanging drop, temperature 298K
|
Resolution 1.70 Å R-free 0.233 |
| 4FT2 crystal structure of Zea mays ZMET2 in complex H3(1-15)K9me2 peptide and SAH Deposited 2012-06-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain P
16–30（15 aa）
Fragment：histone H3 peptide, UNP residues 16-30
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.2 M calcium acetate, 0.1 M imidazole pH 8.0, and 10% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 3.20 Å R-free 0.277 |
| 4FT4 crystal structure of Zea mays ZMET2 in complex H3(1-32)K9me2 peptide and SAH Deposited 2012-06-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain Q
33–64（32 aa）
Fragment：histone H3 peptide, UNP residues 33-64
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.2 M sodium citrate, 0.1 M bis-tris propane, pH 6.5 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.70 Å R-free 0.248 |
| 4FT4 crystal structure of Zea mays ZMET2 in complex H3(1-32)K9me2 peptide and SAH Deposited 2012-06-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain P
33–64（32 aa）
Fragment：histone H3 peptide, UNP residues 33-64
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.2 M sodium citrate, 0.1 M bis-tris propane, pH 6.5 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.70 Å R-free 0.248 |
| 4FWF Complex structure of LSD2/AOF1/KDM1b with H3K4 mimic Deposited 2012-07-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
2–21（20 aa）
Fragment：UNP residues 2-21
|
Mutation：K4M | ZN ZINC ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；298 K；21% PEG3350, 200mM diammonium citrate, pH 7, VAPOR DIFFUSION, temperature 298K
|
Resolution 2.70 Å R-free 0.237 |
| 4LK9 Crystal Structure of MOZ double PHD finger histone H3 tail complex Deposited 2013-07-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–22（21 aa）
Fragment：unp residues 2-22
|
Not recorded | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；283 K；100 mM Na-Hepes, 1.4 M sodium citrate, pH 7.5, VAPOR DIFFUSION, temperature 283K
|
Resolution 1.60 Å R-free 0.186 |
| 4LKA Crystal Structure of MOZ double PHD finger histone H3K9ac complex Deposited 2013-07-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–22（21 aa）
Fragment：unp residues 2-22
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；283 K；100 mM Na-Hepes, 1.4 M sodium citrate, pH 7.5, vapor diffusion, temperature 283K
|
Resolution 1.61 Å R-free 0.185 |
| 4LLB Crystal Structure of MOZ double PHD finger histone H3K14ac complex Deposited 2013-07-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
2–22（21 aa）
Fragment：unp residues 2-22
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.5；283 K；100 mM Tris-Cl, 200 mM Li2SO4, 30% PEG 4000, pH 8.5, VAPOR DIFFUSION, temperature 283K
|
Resolution 2.50 Å R-free 0.266 |
| 4LLB Crystal Structure of MOZ double PHD finger histone H3K14ac complex Deposited 2013-07-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
2–22（21 aa）
Fragment：unp residues 2-22
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.5；283 K；100 mM Tris-Cl, 200 mM Li2SO4, 30% PEG 4000, pH 8.5, VAPOR DIFFUSION, temperature 283K
|
Resolution 2.50 Å R-free 0.266 |
| 4N4H Crystal structure of the Bromo-PWWP of the mouse zinc finger MYND-type containing 11 isoform alpha in complex with histone H3.1K36me3 Deposited 2013-10-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
22–43（22 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.3；289 K；25% (w/v) polyethylene glycol 4000, 0.1M Tris-HCl, pH 8.3, 0.2M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 2.30 Å R-free 0.263 |
| 4UP0 Ternary crystal structure of the Pygo2 PHD finger in complex with the B9L HD1 domain and a H3K4me2 peptide Deposited 2014-06-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
2–16（15 aa）
Fragment：RESIDUES 2-16
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
1 M SODIUM CITRATE, 0.1 M TRIS PH 7, 0.2 M NACL
|
Resolution 1.28 Å R-free 0.166 |
| 4YM5 Crystal structure of the human nucleosome containing 6-4PP (inside) Deposited 2015-03-06 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 4.00 Å R-free 0.289 |
| 4YM6 Crystal structure of the human nucleosome containing 6-4PP (outside) Deposited 2015-03-06 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 3.51 Å R-free 0.287 |
| 4Z0R Crystal Structure of the CW domain of ZCWPW2 mutant F78R in complex with histone H3 peptide Deposited 2015-03-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
2–16（15 aa）
Fragment：N-terminal tail (UNP residues 2-16)
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 UNX UNKNOWN LIGAND × 9 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；2 M ammonium sulfate, 2% PEG400, 0.1 M HEPES sodium
|
Resolution 1.75 Å R-free 0.192 |
| 4Z2M Crystal structure of human SPT16 Mid-AID/H3-H4 tetramer FACT Histone complex Deposited 2015-03-30 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain G
35–136（102 aa）
Fragment：UNP residues 35-136
Chain I
35–136（102 aa）
Fragment：UNP residues 35-136
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；10% PEG400, 0.9-1.1 M Imidazole, 100-150 mM L-histidine
|
Resolution 2.98 Å R-free 0.246 |
| 5AV5 human nucleosome core particle Deposited 2015-06-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | MN MANGANESE (II) ION × 14 |
X-RAY DIFFRACTION
X-ray crystallization conditions
LIQUID DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
|
Resolution 2.40 Å R-free 0.233 |
| 5AV6 human nucleosome core particle Deposited 2015-06-12 | Different construct Different 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 | MN MANGANESE (II) ION × 14 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
|
Resolution 2.20 Å R-free 0.229 |
| 5AV8 human nucleosome core particle Deposited 2015-06-12 | Different construct Different 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 | MN MANGANESE (II) ION × 14 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
|
Resolution 2.20 Å R-free 0.233 |
| 5AV9 human nucleosome core particle Deposited 2015-06-12 | Different construct Different 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 | MN MANGANESE (II) ION × 14 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
|
Resolution 2.20 Å R-free 0.239 |
| 5AVB human nucleosome core particle Deposited 2015-06-12 | Different construct Different 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 | MN MANGANESE (II) ION × 14 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
|
Resolution 2.40 Å R-free 0.236 |
| 5AVC human nucleosome core particle Deposited 2015-06-12 | Different construct Different 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 | MN MANGANESE (II) ION × 14 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
|
Resolution 2.40 Å R-free 0.238 |
| 5B24 The crystal structure of the nucleosome containing cyclobutane pyrimidine dimer Deposited 2015-12-31 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 3.60 Å R-free 0.249 |
| 5B2I Human nucleosome containing CpG unmethylated DNA Deposited 2016-01-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | MN MANGANESE (II) ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
|
Resolution 3.00 Å R-free 0.257 |
| 5B2J Human nucleosome containing CpG methylated DNA Deposited 2016-01-18 | Different construct Different 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 | MN MANGANESE (II) ION × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
|
Resolution 2.60 Å R-free 0.252 |
| 5B31 The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.1. Deposited 2016-02-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | MN MANGANESE (II) ION × 8 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.20 Å R-free 0.271 |
| 5C3I Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2 Deposited 2015-06-17 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain J
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0
|
Resolution 3.50 Å R-free 0.253 |
| 5C3I Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2 Deposited 2015-06-17 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0
|
Resolution 3.50 Å R-free 0.253 |
| 5C3I Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2 Deposited 2015-06-17 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain F
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0
|
Resolution 3.50 Å R-free 0.253 |
| 5C3I Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2 Deposited 2015-06-17 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain N
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0
|
Resolution 3.50 Å R-free 0.253 |
| 5C3I Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2 Deposited 2015-06-17 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain R
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0
|
Resolution 3.50 Å R-free 0.253 |
| 5C3I Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2 Deposited 2015-06-17 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain V
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0
|
Resolution 3.50 Å R-free 0.253 |
| 5CPI Nucleosome containing unmethylated Sat2R DNA Deposited 2015-07-21 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.90 Å R-free 0.295 |
| 5CPJ Nucleosome containing methylated Sat2R DNA Deposited 2015-07-21 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 3.15 Å R-free 0.295 |
| 5CPK Nucleosome containing methylated Sat2L DNA Deposited 2015-07-21 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.63 Å R-free 0.284 |
| 5GSE Crystal structure of unusual nucleosome Deposited 2016-08-16 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric |
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 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；potassium bromide, potassium thiocyanate, Tris-HCl, PGA-LM, PEG 400
|
Resolution 3.14 Å R-free 0.255 |
| 5GSU Crystal structure of nucleosome core particle consisting of human testis-specific histone variants, Th2A and Th2B Deposited 2016-08-17 | Different construct Different 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 | CL CHLORIDE ION × 3 MN MANGANESE (II) ION × 15 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；20mM Pottasium Cacodylate pH 6.0, 60-70mM KCl, 70-90mM MnCl2
|
Resolution 3.10 Å R-free 0.257 |
| 5GT0 Crystal structure of nucleosome complex with human testis-specific histone variants, Th2a Deposited 2016-08-18 | Different construct Different 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 | MN MANGANESE (II) ION × 14 CL CHLORIDE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；60-70mM KCl, 70-90mM MnCl2, 24% MPD
|
Resolution 2.82 Å R-free 0.280 |
| 5GT3 Crystal structure of nucleosome particle in the presence of human testis-specific histone variant, hTh2b Deposited 2016-08-18 | Different construct Different 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 | MN MANGANESE (II) ION × 12 CL CHLORIDE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；60-70mM KCl, 70-90mM MnCl2, 24% MPD
|
Resolution 2.91 Å R-free 0.258 |
| 5GTC Crystal structure of complex between DMAP-SH conjugated with a Kaposi's sarcoma herpesvirus LANA peptide (5-15) and nucleosome core particle Deposited 2016-08-19 | Different construct Different 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 | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.70 Å R-free 0.267 |
| 5HJB AF9 YEATS in complex with histone H3 Crotonylation at K9 Deposited 2016-01-12 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
4–11（8 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；20% (w/v) polyethylene glycol 4000, 0.2 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, 3% MPD
|
Resolution 2.70 Å R-free 0.253 |
| 5HJC BRD3 second bromodomain in complex with histone H3 acetylation at K18 Deposited 2016-01-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
16–24（9 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；30%(w/v) polyethylene glycol methyl ether 5000, 0.2 M ammonium sulfate, 0.1 M MES, 0.1 M guanidine hydrochloride
|
Resolution 2.60 Å R-free 0.269 |
| 5HJD AF9 YEATS in complex with histone H3 Crotonylation at K18 Deposited 2016-01-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain B
15–21（7 aa）
Chain D
15–21（7 aa）
Chain F
15–21（7 aa）
Chain L
15–21（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 3 SO4 SULFATE ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；20%(w/v) polyethylene glycol 4000, 0.2 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, 0.1 M copper chloride dihydrate
|
Resolution 2.81 Å R-free 0.273 |
| 5HJD AF9 YEATS in complex with histone H3 Crotonylation at K18 Deposited 2016-01-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain H
15–21（7 aa）
Chain I
15–21（7 aa）
Chain J
15–21（7 aa）
Chain M
15–21（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 1 SO4 SULFATE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；20%(w/v) polyethylene glycol 4000, 0.2 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, 0.1 M copper chloride dihydrate
|
Resolution 2.81 Å R-free 0.273 |
| 5IQL Crystal structure of YEATS2 YEATS bound to H3K27cr peptide Deposited 2016-03-11 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
25–32（8 aa）
Fragment：H3 peptide (UNP RESIDUES 25-32)
|
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；0.1M Bis-Tris propane, 4.0 M NH4Ac, pH 7.0
|
Resolution 2.10 Å R-free 0.253 |
| 5J9S ENL YEATS in complex with histone H3 acetylation at K27 Deposited 2016-04-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
16–40（25 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.1M K/Na Tartrate, 0.1M Sodium citrate tribasic dihydrate, pH 5.6, 2M (NH4)2SO4
|
Resolution 2.70 Å R-free 0.210 |
| 5JRG Crystal structure of the nucleosome containing the DNA with tetrahydrofuran (THF) Deposited 2016-05-06 | 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 × 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 × 15 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.50 Å R-free 0.245 |
| 5KKL Structure of ctPRC2 in complex with H3K27me3 and H3K27M Deposited 2016-06-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
23–31（9 aa）
|
Mutation：K2027M | ZN ZINC ION × 8 SAM S-ADENOSYLMETHIONINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；15% PEG4000, 175mM ammonium citrate, pH 7.0
|
Resolution 2.94 Å R-free 0.234 |
| 5T1G chromo shadow domain of CBX1 in complex with a histone peptide Deposited 2016-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
39–53（15 aa）
Fragment：unp residues 39-53
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | UNX UNKNOWN LIGAND × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.5 M sodium citrate, 0.1 M HEPES
|
Resolution 1.90 Å R-free 0.243 |
| 5T1I CBX3 chromo shadow domain in complex with histone H3 peptide Deposited 2016-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
39–53（15 aa）
Fragment：unp residues 39-53
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | UNX UNKNOWN LIGAND × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；25% PEG 3350, 0.2 M sodium chloride, 0.1 M Hepes, 5% Ethylene Glycol
|
Resolution 1.60 Å R-free 0.239 |
| 5T8R Crystal structure of human BAZ2A PHD zinc finger in complex with unmodified H3 10-mer Deposited 2016-09-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
2–11（10 aa）
Fragment：UNP residues 2-11
|
Not recorded | ZN ZINC ION × 2 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；2.2 M Na/K phosphate
|
Resolution 2.40 Å R-free 0.235 |
| 5T8R Crystal structure of human BAZ2A PHD zinc finger in complex with unmodified H3 10-mer Deposited 2016-09-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
2–11（10 aa）
Fragment：UNP residues 2-11
|
Not recorded | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；2.2 M Na/K phosphate
|
Resolution 2.40 Å R-free 0.235 |
| 5T8R Crystal structure of human BAZ2A PHD zinc finger in complex with unmodified H3 10-mer Deposited 2016-09-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain G
2–11（10 aa）
Fragment：UNP residues 2-11
|
Not recorded | ZN ZINC ION × 4 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；2.2 M Na/K phosphate
|
Resolution 2.40 Å R-free 0.235 |
| 5T8R Crystal structure of human BAZ2A PHD zinc finger in complex with unmodified H3 10-mer Deposited 2016-09-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
2–11（10 aa）
Fragment：UNP residues 2-11
|
Not recorded | ZN ZINC ION × 4 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；2.2 M Na/K phosphate
|
Resolution 2.40 Å R-free 0.235 |
| 5TBN Solution NMR structure of PHF20 PHD domain in complex with a histone H3K4me2 peptide Deposited 2016-09-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
2–12（11 aa）
Fragment：residues 2-12
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
SOLUTION NMR
NMR measurement conditions
pH 7；298 K；Ionic strength (raw mmCIF value) 20 mM sodium phosphate；Pressure 101325
NMR sample composition
1.5 mM [U-15N] PHF20 PHD domain, 6.0 mM H3K4me2 peptide, 25 mM sodium phosphate, 0.3 mM DSS, 1.5 mM sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
1.5 mM [U-13C; U-15N] PHF20 PHD domain, 6.0 mM H3K4me2 peptide, 25 mM sodium phosphate, 0.3 mM DSS, 1.5 mM sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
2 mM H3K4me2 peptide, 25 mM sodium phosphate, 0.3 mM DSS, 1.5 mM sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 5VA6 CRYSTAL STRUCTURE OF ATXR5 IN COMPLEX WITH HISTONE H3.1 MONO-METHYLATED ON R26 Deposited 2017-03-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
20–37（18 aa）
Fragment：residues 20-37
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；50% polypropylene glycol 400, 5% DMSO, 0.1 M HEPES-NaOH (pH 6.0)
|
Resolution 2.40 Å R-free 0.297 |
| 5VA6 CRYSTAL STRUCTURE OF ATXR5 IN COMPLEX WITH HISTONE H3.1 MONO-METHYLATED ON R26 Deposited 2017-03-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
20–37（18 aa）
Fragment：residues 20-37
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；50% polypropylene glycol 400, 5% DMSO, 0.1 M HEPES-NaOH (pH 6.0)
|
Resolution 2.40 Å R-free 0.297 |
| 5WFC Humanized mutant of the Chaetomium thermophilum Polycomb Repressive Complex 2 bound to the inhibitor GSK343 Deposited 2017-07-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
23–33（11 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 8 A97 N-[(6-methyl-2-oxo-4-propyl-1,2-dihydropyridin-3-yl)methyl]-6-[2-(4-methylpiperazin-1-yl)pyridin-4-yl]-1-(propan-2-yl)-1H-indazole-4-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；100 mM sodium malonate pH 7.0, 16% PEG 3350, 43 mM 3-cyclohexyl-1-propylphosphocholine
|
Resolution 2.28 Å R-free 0.203 |
| 5WVO Crystal structure of DNMT1 RFTS domain in complex with K18/K23 mono-ubiquitylated histone H3 Deposited 2016-12-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain D
2–37（36 aa）
Fragment：UNP residues 2-37
|
Mutation：K18C,K23C | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；100mM Bis-Tris (pH 6.0), 200mM lithium sulfate monohydrate, 20% PEG 10000
|
Resolution 2.00 Å R-free 0.239 |
| 5XF3 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,R-configuration) Deposited 2017-04-07 | Different construct Different 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 | MG MAGNESIUM ION × 1 RUD [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 × 2 RRK (1R,2R)-1,2-diphenylethane-1,2-diamine × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；35-55 mM MnCl2, 25-49 mM KCl, 20 mM K-Cacodylate pH 6.0
|
Resolution 2.60 Å R-free 0.270 |
| 5XF4 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (S,S-configuration) Deposited 2017-04-07 | Different construct Different 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 | MG MAGNESIUM ION × 1 RUD [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 × 2 SSK (1S,2S)-1,2-diphenylethane-1,2-diamine × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；35-55 mM MnCl2, 25-49 mM KCl, 20 mM K-Cacodylate pH 6.0
|
Resolution 2.87 Å R-free 0.266 |
| 5XF5 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,S-configuration) Deposited 2017-04-07 | Different construct Different 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 | MG MAGNESIUM ION × 1 RUD [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 × 2 RSK (1S,2R)-1,2-diphenylethane-1,2-diamine × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；35-55mM MnCl2, 25-49mM KCl, 20mM K-Cacodylate pH 6.0
|
Resolution 2.82 Å R-free 0.264 |
| 5XFR Ternary complex of MTF2, DNA and histone Deposited 2017-04-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric |
Chain C
34–41（8 aa）
Chain D
34–41（8 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M MES monohydrate-pH 6.5, 0.2M ammonium sulfate, 25% PEG monomethyl ether 5000, 10% glycerol
|
Resolution 2.25 Å R-free 0.231 |
| 5Y0C Crystal Structure of the human nucleosome at 2.09 angstrom resolution Deposited 2017-07-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | MN MANGANESE (II) ION × 10 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.09 Å R-free 0.249 |
| 5Y0D Crystal Structure of the human nucleosome containing the H2B E76K mutant Deposited 2017-07-16 | Different construct Different 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 | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 10 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 1.99 Å R-free 0.252 |
| 5Z23 Crystal structure of the nucleosome containing a chimeric histone H3/CENP-A CATD Deposited 2017-12-28 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–75（75 aa）
Chain A
114–136（23 aa）
Chain E
1–75（75 aa）
Chain E
114–136（23 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.73 Å R-free 0.261 |
| 5Z30 The crystal structure of the nucleosome containing a cancer-associated histone H2A.Z R80C mutant Deposited 2018-01-05 | Different construct Different 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 | CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.45 Å R-free 0.243 |
| 5ZBX The crystal structure of the nucleosome containing histone H3.1 CATD(V76Q, K77D) Deposited 2018-02-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–75（75 aa）
Chain A
114–136（23 aa）
Chain E
1–75（75 aa）
Chain E
114–136（23 aa）
|
Mutation：V76Q, K77D Mutation：V76Q, K77D Mutation：V76Q, K77D Mutation：V76Q, K77D | CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.58 Å R-free 0.249 |
| 6BHD Crystal structure of SETDB1 with a modified H3 peptide Deposited 2017-10-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
5–20（16 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | UNX UNKNOWN LIGAND × 35 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；291 K；25% PEG3350, 0.2 M sodium chloride, 0.1 M HEPES, 5% glycerol
|
Resolution 1.25 Å R-free 0.183 |
| 6BHE Crystal structure of SETDB1 with a modified H3 peptide Deposited 2017-10-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
5–20（16 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | UNX UNKNOWN LIGAND × 36 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；291 K；25% PEG3350, 0.2 M sodium chloride, 0.1 M HEPES, 5% glycerol
|
Resolution 1.35 Å R-free 0.172 |
| 6BHG Crystal structure of SETDB1 with a modified H3 peptide Deposited 2017-10-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
5–20（16 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | UNX UNKNOWN LIGAND × 40 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6.5；291 K；20% PEG5000 MME, 0.1 M Bis-Tris
|
Resolution 1.45 Å R-free 0.176 |
| 6BHH Crystal structure of SETDB1 with a modified H3 peptide Deposited 2017-10-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
5–20（16 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 2 UNX UNKNOWN LIGAND × 26 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；291 K；25% PEG3350, 0.2 M lithium sulfate, 0.1 M HEPES
|
Resolution 1.85 Å R-free 0.237 |
| 6BHI Crystal structure of SETDB1 with a modified H3 peptide Deposited 2017-10-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
5–20（16 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | UNX UNKNOWN LIGAND × 35 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；291 K；25% PEG3350, 0.2 M lithium sulfate, 0.1 M HEPES
|
Resolution 1.40 Å R-free 0.187 |
| 6D07 Crystal structure of the complex between human chromobox homolog 1 (CBX1) and H3K9me3 peptide Deposited 2018-04-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
2–16（15 aa）
Fragment：H3K9(me)3 peptide (UNP residues 2-16)
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.2 M sodium chloride, 0.1 M Tris, pH 8.0, 30% w/v PEG3350
|
Resolution 2.10 Å R-free 0.257 |
| 6D07 Crystal structure of the complex between human chromobox homolog 1 (CBX1) and H3K9me3 peptide Deposited 2018-04-10 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
2–16（15 aa）
Fragment：H3K9(me)3 peptide (UNP residues 2-16)
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.2 M sodium chloride, 0.1 M Tris, pH 8.0, 30% w/v PEG3350
|
Resolution 2.10 Å R-free 0.257 |
| 6D08 Crystal structure of an engineered bump-hole complex of mutant human chromobox homolog 1 (CBX1) with H3K9bn peptide Deposited 2018-04-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
2–16（15 aa）
Fragment：H3K9bn peptide (UNP residues 2-16)
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | GOL GLYCEROL × 2 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M citrate, pH 5.0, 3 M ammonium sulfate
|
Resolution 2.10 Å R-free 0.252 |
| 6D08 Crystal structure of an engineered bump-hole complex of mutant human chromobox homolog 1 (CBX1) with H3K9bn peptide Deposited 2018-04-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
2–16（15 aa）
Fragment：H3K9bn peptide (UNP residues 2-16)
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | GOL GLYCEROL × 2 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M citrate, pH 5.0, 3 M ammonium sulfate
|
Resolution 2.10 Å R-free 0.252 |
| 6HKT Structure of an H1-bound 6-nucleosome array Deposited 2018-09-08 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 48 PDB declaration: 50-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 U
1–136（136 aa）
Chain Y
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）
Chain u
1–136（136 aa）
Chain y
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.8；293.15 K；15% MPD, 0.1 M NaCl and 0.1 M Tris pH 8.8
|
Resolution 9.70 Å R-free 0.286 |
| 6HTS Cryo-EM structure of the human INO80 complex bound to nucleosome Deposited 2018-10-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric |
Chain I
1–136（136 aa）
Chain M
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 6 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.80 Å |
| 6IPU Human nucleosome core particle containing 145 bp of DNA Deposited 2018-11-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
39–136（98 aa）
Chain E
39–136（98 aa）
|
Not recorded | CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；manganese chloride, potassium chloride, potassium cacodylate
|
Resolution 1.99 Å R-free 0.263 |
| 6IQ4 Nucleosome core particle cross-linked with a hetero-binuclear molecule possessing RAPTA and gold(I) 4-(diphenylphosphino)benzoic acid groups. Deposited 2018-11-06 | Different construct Different 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
39–136（98 aa）
Chain E
39–136（98 aa）
|
Not recorded | AU GOLD ION × 1 XIS 4-diphenylphosphanylbenzoic acid × 1 MG MAGNESIUM ION × 4 D0X [Ru(eta(6)-p-cymene)Cl-2(pta) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；manganese chloride, potassium chloride, potassium cacodylate
|
Resolution 2.25 Å R-free 0.257 |
| 6JOU Crystal structure of the human nucleosome containing H2A.Z.1 S42R Deposited 2019-03-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | MN MANGANESE (II) ION × 9 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.17 Å R-free 0.250 |
| 6JR0 Crystal structure of the human nucleosome phased with 12 selenium atoms Deposited 2019-04-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.50 Å R-free 0.253 |
| 6JR1 Crystal structure of the human nucleosome phased with 16 selenium atoms Deposited 2019-04-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain 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 × 4 MN MANGANESE (II) ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.40 Å R-free 0.243 |
| 6JXD Human nucleosome core particle with cohesive end DNA termini Deposited 2019-04-23 | Different construct Different 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
39–136（98 aa）
Chain E
39–135（97 aa）
|
Not recorded | MN MANGANESE (II) ION × 17 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；manganese chloride, potassium chloride, potassium cacodylate
|
Resolution 2.25 Å R-free 0.292 |
| 6K1I Human nucleosome core particle with gammaH2A.X variant Deposited 2019-05-10 | Different construct Different 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 | CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 23 K POTASSIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；potassium chloride, manganese chloride, potassium cacodylate
|
Resolution 2.75 Å R-free 0.277 |
| 6K1J Human nucleosome core particle with H2A.X variant Deposited 2019-05-10 | Different construct Different 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 | CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；Potassium Chloride, Manganese Chloride, Potassium Cacodylate
|
Resolution 2.85 Å R-free 0.319 |
| 6K1K Human nucleosome core particle with H2A.X S139E variant Deposited 2019-05-10 | Different construct Different 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 | CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 33 K POTASSIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；potassium chloride, manganese chloride, potassium cacodylate
|
Resolution 2.20 Å R-free 0.275 |
| 6KE9 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-07-04 | Different construct Different 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 | MN MANGANESE (II) ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
|
Resolution 2.22 Å R-free 0.230 |
| 6KVD Crystal structure of human nucleosome containing H2A.J Deposited 2019-09-04 | Different construct Different 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 | MN MANGANESE (II) ION × 13 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.21 Å R-free 0.257 |
| 6L49 H3-CA-H3 tri-nucleosome with the 22 base-pair linker DNA Deposited 2019-10-16 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric |
Chain K
1–136（136 aa）
Chain O
1–136（136 aa）
Chain S
1–136（136 aa）
Chain W
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 18.90 Å |
| 6L4A H3-H3-H3 tri-nucleosome with the 22 base-pair linker DNA Deposited 2019-10-16 | Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-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 S
1–136（136 aa）
Chain W
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 12.30 Å |
| 6L9H The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-11-10 | Different construct Different 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 | MN MANGANESE (II) ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
|
Resolution 2.60 Å R-free 0.278 |
| 6L9Z 338 bp di-nucleosome assembled with linker histone H1.X Deposited 2019-11-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric |
Chain 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 | CL CHLORIDE ION × 8 CA CALCIUM ION × 65 K POTASSIUM ION × 10 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；Calcium chloride, Potassium chloride, Potassium Cacodylate
|
Resolution 2.50 Å R-free 0.256 |
| 6LA2 343 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 Deposited 2019-11-11 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 34 PDB declaration: 38-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 U
1–136（136 aa）
Chain Y
1–136（136 aa）
Chain e
1–136（136 aa）
Chain i
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, Potassium chloride, Sodium acetate
|
Resolution 3.89 Å R-free 0.267 |
| 6LA8 349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 Deposited 2019-11-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric |
Chain 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 | CA CALCIUM ION × 23 K POTASSIUM ION × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate (cryo-25% MPD)
|
Resolution 3.40 Å R-free 0.265 |
| 6LA9 349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 (high cryoprotectant) Deposited 2019-11-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric |
Chain 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 | CA CALCIUM ION × 40 K POTASSIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
|
Resolution 3.70 Å R-free 0.266 |
| 6LAB 169 bp nucleosome, harboring cohesive DNA termini, assembled with linker histone H1.0 Deposited 2019-11-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric |
Chain 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 | CA CALCIUM ION × 20 K POTASSIUM ION × 2 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
|
Resolution 3.20 Å R-free 0.262 |
| 6LE9 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-11-24 | Different construct Different 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 | MN MANGANESE (II) ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
|
Resolution 2.60 Å R-free 0.281 |
| 6LER 169 bp nucleosome harboring non-identical cohesive DNA termini. Deposited 2019-11-26 | Different construct Different 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 | CA CALCIUM ION × 6 K POTASSIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
|
Resolution 3.00 Å R-free 0.261 |
| 6LER 169 bp nucleosome harboring non-identical cohesive DNA termini. Deposited 2019-11-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain K
1–136（136 aa）
Chain O
1–136（136 aa）
|
Not recorded | CA CALCIUM ION × 8 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
|
Resolution 3.00 Å R-free 0.261 |
| 6M3V 355 bp di-nucleosome harboring cohesive DNA termini Deposited 2020-03-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric |
Chain 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 | K POTASSIUM ION × 1 CA CALCIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 4.5；291 K；Calcium chloride, Potassium chloride, Potassium Cacodylate, Poly glutamic acid
|
Resolution 4.60 Å R-free 0.261 |
| 6M44 355 bp di-nucleosome harboring cohesive DNA termini (high cryoprotectant) Deposited 2020-03-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric |
Chain 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 | CA CALCIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；Calcium chloride, Potassium chloride, Potassium Cacodylate, Poly glutamic acid
|
Resolution 3.81 Å R-free 0.286 |
| 6M4D Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2 Deposited 2020-03-06 | Different construct Different mutation/modification Different oligomeric state 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 4.40 Å |
| 6M4G Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2 Deposited 2020-03-06 | Different construct Different mutation/modification Different oligomeric state 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 2.80 Å |
| 6M4H Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2 Deposited 2020-03-07 | Different construct Different mutation/modification Different oligomeric state 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 3.90 Å |
| 6R8Y Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB Deposited 2019-04-02 | Different construct Different mutation/modification Different oligomeric state 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 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 6R8Z Cryo-EM structure of NCP_THF2(-1)-UV-DDB Deposited 2019-04-02 | Different construct Different mutation/modification Different oligomeric state 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 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 6R90 Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A Deposited 2019-04-02 | Different construct Different mutation/modification Different oligomeric state 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 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 6R91 Cryo-EM structure of NCP_THF2(-3)-UV-DDB Deposited 2019-04-02 | Different construct Different mutation/modification Different oligomeric state 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 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 6R92 Cryo-EM structure of NCP-THF2(+1)-UV-DDB class B Deposited 2019-04-02 | Different construct Different mutation/modification Different oligomeric state 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 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.80 Å |
| 6R93 Cryo-EM structure of NCP-6-4PP Deposited 2019-04-02 | Different construct Different mutation/modification Different oligomeric state 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 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 6R94 Cryo-EM structure of NCP_THF2(-3) Deposited 2019-04-02 | Different construct Different mutation/modification Different oligomeric state 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 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 6T90 OCT4-SOX2-bound nucleosome - SHL-6 Deposited 2019-10-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–134（134 aa）
|
Not recorded | PTD PENTANEDIAL × 9 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.05 Å |
| 6T93 Nucleosome with OCT4-SOX2 motif at SHL-6 Deposited 2019-10-25 | Different construct Different mutation/modification Different oligomeric state 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 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.49 Å |
| 6UPK Structure of FACT_subnucleosome complex 1 Deposited 2019-10-17 | Different construct Different mutation/modification Different oligomeric state 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 4.90 Å |
| 6UPL Structure of FACT_subnucleosome complex 2 Deposited 2019-10-17 | Different construct Different mutation/modification Different oligomeric state 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
|
Resolution 7.40 Å |
| 6USJ Structure of two nucleosomes bridged by human PARP2 Deposited 2019-10-27 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-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）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；Buffer was pH-adjusted and filtered through a 0.22 um filter.
cryo-EM vitrification conditions
Cryogen ETHANE；Blot time 2s, blot force 0
|
Resolution 10.50 Å |
| 6V2K The nucleosome structure after H2A-H2B exchange Deposited 2019-11-24 | Different construct Different 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 | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 10 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.60 Å R-free 0.248 |
| 6V41 crystal structure of CDY1 chromodomain bound to H3K9me3 Deposited 2019-11-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain QQQ
2–16（15 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | UNX UNKNOWN LIGAND × 20 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；1.4 M sodium citrate, 0.1 M HEPES
|
Resolution 1.60 Å R-free 0.215 |
| 6V92 RSC-NCP Deposited 2019-12-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 33 PDB declaration: 35-meric |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 20.00 Å |
| 6WAV Crystal structure of PHF1 in complex with H3K36me3 substitution Deposited 2020-03-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
32–43（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 1 UNX UNKNOWN LIGAND × 17 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；1.2 M ammonium sulfate and 0.1 M sodium acetate 4.6
|
Resolution 1.70 Å R-free 0.241 |
| 6WAV Crystal structure of PHF1 in complex with H3K36me3 substitution Deposited 2020-03-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
32–43（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | UNX UNKNOWN LIGAND × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；1.2 M ammonium sulfate and 0.1 M sodium acetate 4.6
|
Resolution 1.70 Å R-free 0.241 |
| 6WAV Crystal structure of PHF1 in complex with H3K36me3 substitution Deposited 2020-03-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
32–43（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | UNX UNKNOWN LIGAND × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；1.2 M ammonium sulfate and 0.1 M sodium acetate 4.6
|
Resolution 1.70 Å R-free 0.241 |
| 6WAV Crystal structure of PHF1 in complex with H3K36me3 substitution Deposited 2020-03-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain H
32–43（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | UNX UNKNOWN LIGAND × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；1.2 M ammonium sulfate and 0.1 M sodium acetate 4.6
|
Resolution 1.70 Å R-free 0.241 |
| 6WW4 Crystal structure of HERC2 ZZ domain in complex with histone H3 tail Deposited 2020-05-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
2–7（6 aa）
Fragment：fusion protein
|
Not recorded | ZN ZINC ION × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, and 17% PEG 10000
|
Resolution 2.25 Å R-free 0.243 |
| 6WW4 Crystal structure of HERC2 ZZ domain in complex with histone H3 tail Deposited 2020-05-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–7（6 aa）
Fragment：fusion protein
|
Not recorded | ZN ZINC ION × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, and 17% PEG 10000
|
Resolution 2.25 Å R-free 0.243 |
| 6YIH Structure of Chromosomal Passenger Complex (CPC) bound to phosphorylated Histone 3 peptide at 2.6 A. Deposited 2020-04-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain D
2–13（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；291 K；20 % (w/v) PEG 4,000, 100 mM HEPES pH 7.0, 150 mM ammonium sulphate
|
Resolution 2.55 Å R-free 0.259 |
| 6YOV OCT4-SOX2-bound nucleosome - SHL+6 Deposited 2020-04-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–134（134 aa）
|
Not recorded | PTD PENTANEDIAL × 8 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.42 Å |
| 7BWD Structure of Dot1L-H2BK34ub Nucleosome Complex Deposited 2020-04-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 4.32 Å |
| 7C0M Human cGAS-nucleosome complex Deposited 2020-05-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
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 3.90 Å |
| 7CCQ Structure of the 1:1 cGAS-nucleosome complex Deposited 2020-06-17 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
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 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7CCR Structure of the 2:2 cGAS-nucleosome complex Deposited 2020-06-17 | Different construct Different mutation/modification Different oligomeric state Different 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 L
39–136（98 aa）
Chain P
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 4.90 Å |
| 7COW 353 bp di-nucleosome harboring cohesive DNA termini with linker histone H1.0 Deposited 2020-08-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric |
Chain 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 | CA CALCIUM ION × 3 K POTASSIUM ION × 5 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；potassium acetate, calcium chloride, potassium chloride
|
Resolution 2.86 Å R-free 0.297 |
| 7D1Z Cryo-EM structure of SET8-nucleosome complex Deposited 2020-09-15 | Different construct Different mutation/modification Different oligomeric state 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 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.15 Å |
| 7DBP Linker histone defines structure and self-association behaviour of the 177 bp human chromosome Deposited 2020-10-21 | Different construct Different mutation/modification Different oligomeric state 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
|
Resolution 4.50 Å |
| 7E8D NSD2 E1099K mutant bound to nucleosome Deposited 2021-03-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | ZN ZINC ION × 3 SFG SINEFUNGIN × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 7K5X Cryo-EM structure of a chromatosome containing human linker histone H1.0 Deposited 2020-09-17 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
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 2.93 Å |
| 7K5Y Cryo-EM structure of a chromatosome containing human linker histone H1.4 Deposited 2020-09-17 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
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 2.76 Å |
| 7K60 Cryo-EM structure of a chromatosome containing human linker histone H1.10 Deposited 2020-09-17 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
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 3.12 Å |
| 7K61 Cryo-EM structure of 197bp nucleosome aided by scFv Deposited 2020-09-17 | Different construct Different mutation/modification Different oligomeric state 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 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.85 Å |
| 7K63 Cryo-EM structure of a chromatosome containing chimeric linker histone gH1.10-ncH1.4 Deposited 2020-09-18 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
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 3.03 Å |
| 7KLR Solution structure of the PHD1 domain of histone demethylase KDM5A in complex with a histone H3(1-10) peptide Deposited 2020-10-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–11（10 aa）
|
Not recorded | ZN ZINC ION × 2 |
SOLUTION NMR
NMR measurement conditions
pH 7.5；298 K；Ionic strength (raw mmCIF value) 150；Pressure 1
NMR sample composition
900 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 4000 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition
550 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 800 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition
1250 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 400 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2, 95% H2O/5% D2O | 95% H2O/5% D2O
|
Resolution not provided |
| 7LBK Crystal structure of human Survivin bound to histone H3 T3phK4me3 peptide Deposited 2021-01-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
2–13（12 aa）
Chain D
2–13（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；The crystal was obtained by mixing 1 uL of protein at 10 mg/mL with 1 uL of mother liquor composed of 0.16 M potassium/sodium tartrate, 14% PEG 3350.
|
Resolution 2.70 Å R-free 0.253 |
| 7LBO Crystal structure of human Survivin bound to histone H3 T3phK4me1 peptide Deposited 2021-01-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
2–13（12 aa）
Chain F
2–13（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；1 uL of protein at 10 mg/mL was mixed with 1 uL of buffer composed of 0.16 M potassium/sodium tartrate, 12% PEG 3350
|
Resolution 2.50 Å R-free 0.261 |
| 7LBP Crystal structure of human Survivin bound to histone H3T3phK4ac peptide Deposited 2021-01-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
2–13（12 aa）
Chain D
2–13（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；1 uL of protein at 10mg/mL was mixed with 1 uL of buffer composed of 0.16 M potassium/sodium tartrate, 12% PEG 3350
|
Resolution 2.60 Å R-free 0.247 |
| 7LBQ Crystal structure of human Survivin bound to histone H3 T3phK4me2 peptide Deposited 2021-01-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain E
2–13（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；1 uL of protein was mixed with 1uL of buffer composed of 2.25 mM spermine, 9 mM MgCl2, 0.9 mM spermidine, 1.8 mM cobalt (III)hexamine chloride, 0.05 sodium cacodylate pH 7.0, 5% PEG 400
|
Resolution 2.69 Å R-free 0.268 |
| 7LYA Cryo-EM structure of the human nucleosome core particle with linked histone proteins H2A and H2B Deposited 2021-03-06 | Different construct Different mutation/modification Different oligomeric state 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 2.91 Å |
| 7LYB Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c Deposited 2021-03-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.28 Å |
| 7LYC Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A Lys13 and Lys15 in complex with BARD1 (residues 415-777) Deposited 2021-03-06 | Different construct Different mutation/modification Different oligomeric state 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
|
Resolution 2.94 Å |
| 7MJU Crystal structure of human AF10 PZP bound to histone H3 tail Deposited 2021-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–14（13 aa）
|
Not recorded | ZN ZINC ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.09 M Tris, 22.5% PEG 3350, and 10 mM spermine tetrahydrochloride
|
Resolution 2.10 Å R-free 0.206 |
| 7NL0 Cryo-EM structure of the Lin28B nucleosome core particle Deposited 2021-02-19 | Different construct Different mutation/modification Different oligomeric state 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 3.50 Å |
| 7SCY Nuc147 bound to single BRCT Deposited 2021-09-29 | Different construct Different mutation/modification Different oligomeric state 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
|
Resolution 4.10 Å |
| 7SCZ Nuc147 bound to multiple BRCTs Deposited 2021-09-29 | Different construct Different mutation/modification Different oligomeric state 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
|
Resolution 3.50 Å |
| 7U0G structure of LIN28b nucleosome bound 3 OCT4 Deposited 2022-02-18 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 13 PDB declaration: pentadecameric |
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 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 7U0I Structure of LIN28b nucleosome bound 2 OCT4 Deposited 2022-02-18 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: tetradecameric |
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 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 7U0J Structure of 162bp LIN28b nucleosome Deposited 2022-02-18 | Different construct Different mutation/modification Different oligomeric state 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 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 7V6Q Crystal structure of sNASP-ASF1A-H3.1-H4 complex Deposited 2021-08-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–136（136 aa）
|
Not recorded | GOL GLYCEROL × 4 1PE PENTAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；18% (v/v) Tacsimate, pH 5.0
11% (v/v) PEG2000MME
|
Resolution 3.00 Å R-free 0.203 |
| 7V6Q Crystal structure of sNASP-ASF1A-H3.1-H4 complex Deposited 2021-08-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain F
1–136（136 aa）
|
Not recorded | GOL GLYCEROL × 2 1PE PENTAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；18% (v/v) Tacsimate, pH 5.0
11% (v/v) PEG2000MME
|
Resolution 3.00 Å R-free 0.203 |
| 7V90 Telomeric mononucleosome Deposited 2021-08-24 | Different construct Different mutation/modification Different oligomeric state 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 6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7V96 Telomeric Dinucleosome Deposited 2021-08-24 | Different construct Different mutation/modification Different oligomeric state Different 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 6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.92 Å |
| 7V9C Telomeric Dinucleosome in open state Deposited 2021-08-24 | Different construct Different mutation/modification Different oligomeric state Different 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 6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 7V9K Telomeric tetranucleosome Deposited 2021-08-25 | Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 34-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 S
1–136（136 aa）
Chain W
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 6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 8.10 Å |
| 7V9S Telomeric trinucleosome in open state Deposited 2021-08-26 | Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-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 S
1–136（136 aa）
Chain W
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 11.00 Å |
| 7VA4 Telomeric tetranucleosome in open state Deposited 2021-08-27 | Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 34-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 S
1–136（136 aa）
Chain W
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 6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 14.00 Å |
| 7VZ4 Cryo-EM structure of human nucleosome core particle composed of the Widom 601L DNA sequence Deposited 2021-11-15 | Different construct Different mutation/modification Different oligomeric state 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 1.89 Å |
| 7W9V Cryo-EM structure of nucleosome in complex with p300 acetyltransferase catalytic core (complex I) Deposited 2021-12-10 | Different construct Different mutation/modification Different oligomeric state 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 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.95 Å |
| 7X57 Cryo-EM structure of human subnucleosome (closed form) Deposited 2022-03-04 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain C
2–136（135 aa）
Chain E
2–136（135 aa）
Chain G
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 3.63 Å |
| 7X58 Cryo-EM structure of human subnucleosome (open form) Deposited 2022-03-04 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain C
2–136（135 aa）
Chain E
2–136（135 aa）
Chain G
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 3.93 Å |
| 7XVL Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an DNA fragment) Deposited 2022-05-24 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
Chain U
1–136（136 aa）
Chain Y
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
|
Resolution 3.51 Å R-free 0.280 |
| 7XVL Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an DNA fragment) Deposited 2022-05-24 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric |
Chain K
1–136（136 aa）
Chain O
1–136（136 aa）
Chain e
1–136（136 aa）
Chain i
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
|
Resolution 3.51 Å R-free 0.280 |
| 7XVM Crystal Structure of Nucleosome-H5 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric |
Chain 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 | CA CALCIUM ION × 18 CL CHLORIDE ION × 3 K POTASSIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
|
Resolution 2.84 Å R-free 0.259 |
| 7XX5 Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric |
Chain 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 | CA CALCIUM ION × 13 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
|
Resolution 3.19 Å R-free 0.259 |
| 7XX6 Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric |
Chain 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 | CA CALCIUM ION × 21 K POTASSIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
|
Resolution 3.39 Å R-free 0.296 |
| 7XX6 Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric |
Chain U
1–136（136 aa）
Chain Y
1–136（136 aa）
Chain e
1–136（136 aa）
Chain i
1–136（136 aa）
|
Not recorded | CA CALCIUM ION × 26 K POTASSIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
|
Resolution 3.39 Å R-free 0.296 |
| 7XZX Cryo-EM structure of the nucleosome in complex with p53 DNA-binding domain Deposited 2022-06-03 | Different construct Different mutation/modification Different oligomeric state 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 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.53 Å |
| 7XZY Cryo-EM structure of the nucleosome containing 193 base-pair DNA with a p53 target sequence Deposited 2022-06-03 | Different construct Different mutation/modification Different oligomeric state 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 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.97 Å |
| 7XZZ Cryo-EM structure of the nucleosome in complex with p53 Deposited 2022-06-03 | Different construct Different mutation/modification Different oligomeric state 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 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.07 Å |
| 7Y00 Cryo-EM structure of the nucleosome containing 169 base-pair DNA with a p53 target sequence Deposited 2022-06-03 | Different construct Different mutation/modification Different oligomeric state 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 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.96 Å |
| 7Y5U Cryo-EM structure of the monomeric human CAF1LC-H3-H4 complex Deposited 2022-06-17 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain D
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7Y5V Cryo-EM structure of the dimeric human CAF1LC-H3-H4 complex Deposited 2022-06-17 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric |
Chain D
1–136（136 aa）
Chain I
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.10 Å |
| 7Y5W Cryo-EM structure of the left-handed Di-tetrasome Deposited 2022-06-17 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain C
1–136（136 aa）
Chain E
1–136（136 aa）
Chain G
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7Y60 Cryo-EM structure of human CAF1LC bound right-handed Di-tetrasome Deposited 2022-06-18 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain C
1–136（136 aa）
Chain E
1–136（136 aa）
Chain G
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7Y61 Cryo-EM structure of the two CAF1LCs bound right-handed Di-tetrasome Deposited 2022-06-18 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain A
1–136（136 aa）
Chain C
1–136（136 aa）
Chain E
1–136（136 aa）
Chain G
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.60 Å |
| 7Y7I chicken KNL2 in complex with the CENP-A nucleosome Deposited 2022-06-22 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–64（64 aa）
Chain E
1–64（64 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.42 Å |
| 7YOZ Cryo-EM structure of human subnucleosome (intermediate form) Deposited 2022-08-02 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain C
2–136（135 aa）
Chain E
2–136（135 aa）
Chain G
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 4.30 Å |
| 7YQK cryo-EM structure of gammaH2AXK15ub-H4K20me2 nucleosome bound to 53BP1 Deposited 2022-08-07 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain A
37–136（100 aa）
Chain E
37–136（100 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.38 Å |
| 7ZI4 Cryo-EM structure of the human INO80 complex bound to a WT nucleosome Deposited 2022-04-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric |
Chain I
1–136（136 aa）
Chain M
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；4uL of sample applied to Quantifoil R2/2 Cu 300 mesh grids. blot parameters were wait time 30 sec, blot time 0.5 sec, blot force -8
|
Resolution 3.20 Å |
| 8DK5 Structure of 187bp LIN28b nucleosome with site 0 mutation Deposited 2022-07-02 | Different construct Different mutation/modification Different oligomeric state 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 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.71 Å |
| 8EVG 162bp CX3CR1 nucleosome (further classified with better nucleosome end) Deposited 2022-10-20 | Different construct Different mutation/modification Different oligomeric state 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 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.75 Å |
| 8EVH CX3CR1 nucleosome and wild type PU.1 complex Deposited 2022-10-20 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-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 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.85 Å |
| 8EVI CX3CR1 nucleosome and PU.1 complex containing disulfide bond mutations Deposited 2022-10-20 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
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 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.64 Å |
| 8EVJ CX3CR1 nucleosome bound PU.1 and C/EBPa Deposited 2022-10-20 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-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 7.1
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 8GE0 Crystal structure of JADE1 PZP domain in complex with Histone H3 Deposited 2023-03-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–14（13 aa）
|
Not recorded | ZN ZINC ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2 M Sodium chloride, 0.1 M HEPES pH 7.0, 20 % w/v PEG 6000
|
Resolution 2.40 Å R-free 0.241 |
| 8GE0 Crystal structure of JADE1 PZP domain in complex with Histone H3 Deposited 2023-03-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
2–14（13 aa）
|
Not recorded | ZN ZINC ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2 M Sodium chloride, 0.1 M HEPES pH 7.0, 20 % w/v PEG 6000
|
Resolution 2.40 Å R-free 0.241 |
| 8GE0 Crystal structure of JADE1 PZP domain in complex with Histone H3 Deposited 2023-03-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
2–14（13 aa）
|
Not recorded | ZN ZINC ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2 M Sodium chloride, 0.1 M HEPES pH 7.0, 20 % w/v PEG 6000
|
Resolution 2.40 Å R-free 0.241 |
| 8GUI Bre1-nucleosome complex (Model I) Deposited 2022-09-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.81 Å |
| 8GUJ Bre1-nucleosome complex (Model II) Deposited 2022-09-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8GUK Human nucleosome core particle (free form) Deposited 2022-09-12 | Different construct Different mutation/modification Different oligomeric state 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 2.51 Å |
| 8H0V RNA polymerase II transcribing a chromatosome (type I) Deposited 2022-09-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric |
Chain a
2–136（135 aa）
Chain e
2–136（135 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 8H0W RNA polymerase II transcribing a chromatosome (type II) Deposited 2022-09-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric |
Chain a
2–136（135 aa）
Chain e
2–136（135 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.60 Å |
| 8H1T Cryo-EM structure of BAP1-ASXL1 bound to chromatosome Deposited 2022-10-04 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
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 3.00 Å |
| 8HAG Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 1 (3.2 angstrom resolution) Deposited 2022-10-26 | Different construct Different mutation/modification Different oligomeric state 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 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8HAH Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 2 (3.9 angstrom resolution) Deposited 2022-10-26 | Different construct Different mutation/modification Different oligomeric state 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 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 8HAI Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 1 (4.7 angstrom resolution) Deposited 2022-10-26 | Different construct Different mutation/modification Different oligomeric state 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 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.70 Å |
| 8HAJ Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 2 (4.8 angstrom resolution) Deposited 2022-10-26 | Different construct Different mutation/modification Different oligomeric state 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 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.80 Å |
| 8HAK Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 4 (4.5 angstrom resolution) Deposited 2022-10-26 | Different construct Different mutation/modification Different oligomeric state 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 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 8HAL Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 1 Deposited 2022-10-26 | Different construct Different mutation/modification Different oligomeric state 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 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.40 Å |
| 8HAM Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 2 Deposited 2022-10-26 | Different construct Different mutation/modification Different oligomeric state 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 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 8HAN Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 3 Deposited 2022-10-26 | Different construct Different mutation/modification Different oligomeric state 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 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 8IEG Bre1(mRBD-RING)/Rad6-Ub/nucleosome complex Deposited 2023-02-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain E
38–135（98 aa）
Chain K
38–135（98 aa）
|
Not recorded | ZN ZINC ION × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.44 Å |
| 8IEJ RNF20-RNF40/hRad6A-Ub/nucleosome complex Deposited 2023-02-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain E
38–135（98 aa）
Chain K
38–135（98 aa）
|
Not recorded | ZN ZINC ION × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.12 Å |
| 8IHL Overlapping tri-nucleosome Deposited 2023-02-23 | Different construct Different oligomeric state 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 K
2–136（135 aa）
Chain M
2–136（135 aa）
Chain Q
2–136（135 aa）
Chain U
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.64 Å |
| 8IIY Crystal structure of MBP fused GAS41 YEATS domain in complex with H3K14ac peptide Deposited 2023-02-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
2–20（19 aa）
Chain C
2–20（19 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Tris buffer (pH 8.5) containing 20% (w/v) PEG monomethyl ether 2000, 200 mM trimethylamine N-oxide
|
Resolution 2.15 Å R-free 0.247 |
| 8IIZ Crystal structure of MBP fused GAS41 YEATS domain in complex with H3K27ac peptide Deposited 2023-02-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
2–33（32 aa）
Chain C
2–33（32 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Tris buffer (pH 8.5) containing 20% (w/v) PEG monomethyl ether 2000, 200 mM trimethylamine N-oxide
|
Resolution 2.10 Å R-free 0.301 |
| 8IJ0 Crystal structure of GAS41 YEATS domain in complex with H3K9ac peptide Deposited 2023-02-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
2–12（11 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | GOL GLYCEROL × 3 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Na-HEPES buffer (pH 7.5) containing 5% (w/v) PEG 400 and 2 M ammonium sulfate
|
Resolution 1.52 Å R-free 0.189 |
| 8IJ0 Crystal structure of GAS41 YEATS domain in complex with H3K9ac peptide Deposited 2023-02-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
2–12（11 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | GOL GLYCEROL × 3 SO4 SULFATE ION × 4 1PE PENTAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Na-HEPES buffer (pH 7.5) containing 5% (w/v) PEG 400 and 2 M ammonium sulfate
|
Resolution 1.52 Å R-free 0.189 |
| 8IQF Cryo-EM structure of the dimeric human CAF1-H3-H4 complex Deposited 2023-03-16 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric |
Chain D
1–136（136 aa）
Chain I
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.60 Å |
| 8IQG Cryo-EM structure of the monomeric human CAF1-H3-H4 complex Deposited 2023-03-16 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain D
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 8J6S Cryo-EM structure of the single CAF-1 bound right-handed Di-tetrasome Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain C
1–136（136 aa）
Chain E
1–136（136 aa）
Chain G
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 8J6T Cryo-EM structure of the double CAF-1 bound right-handed Di-tetrasome Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain A
1–136（136 aa）
Chain C
1–136（136 aa）
Chain E
1–136（136 aa）
Chain G
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.60 Å |
| 8JBX Human canonical 601 DNA nucleosome Deposited 2023-05-09 | Different construct Different mutation/modification Different oligomeric state 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 3.35 Å |
| 8JCC Human histone H2B variant H2BFWT Cryo-EM structure with 601 DNA sequence Deposited 2023-05-10 | Different construct Different mutation/modification Different oligomeric state 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 3.42 Å |
| 8JCD Human H2BFWTH100R nucleosome with 601 DNA Deposited 2023-05-11 | Different construct Different mutation/modification Different oligomeric state 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 3.14 Å |
| 8JHF Native SUV420H1 bound to 167-bp nucleosome Deposited 2023-05-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane
|
Resolution 3.68 Å |
| 8JHG Native SUV420H1 bound to 167-bp nucleosome Deposited 2023-05-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane
|
Resolution 3.58 Å |
| 8JL9 Cryo-EM structure of the human nucleosome with scFv Deposited 2023-06-02 | Different construct Different mutation/modification Different oligomeric state 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 2.65 Å |
| 8JLA Cryo-EM structure of the human nucleosome lacking N-terminal region of H2A, H2B, H3, and H4 Deposited 2023-06-02 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
29–136（108 aa）
Chain E
29–136（108 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.44 Å |
| 8JND The cryo-EM structure of the nonameric RAD51 ring bound to the nucleosome with the linker DNA binding Deposited 2023-06-06 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 19-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 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.66 Å |
| 8JNE The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome without the linker DNA binding Deposited 2023-06-06 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-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 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.68 Å |
| 8JNF The cryo-EM structure of the RAD51 filament bound to the nucleosome Deposited 2023-06-06 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-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 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.91 Å |
| 8KCY Structure of nucleosome complexed with two DEK molecules Deposited 2023-08-08 | Different construct Different mutation/modification Different oligomeric state 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 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8KD1 Structure of nucleosome complexed with one DEK molecule Deposited 2023-08-08 | Different construct Different mutation/modification Different oligomeric state 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 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8KE0 Structure of H1.2 bound to the nucleosome Deposited 2023-08-11 | Different construct Different mutation/modification Different oligomeric state 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 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 8OFF Structure of BARD1 ARD-BRCTs in complex with H2AKc15ub nucleosomes (Map1) Deposited 2023-03-15 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric |
Chain Ca
1–135（135 aa）
Chain Cb
1–135（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM HEPES pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE；blot force = 0 N
blot time = 8 s
|
Resolution 3.40 Å |
| 8OO7 CryoEM Structure INO80core Hexasome complex composite model state1 Deposited 2023-04-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric |
Chain M
2–136（135 aa）
Chain Q
2–136（135 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 7 ALF TETRAFLUOROALUMINATE ION × 1 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；30mM HEPES, pH7.5
50mM NaCl
0.25mM CaCl2
0.25mM DTT
2mM ADP
3.3mM MgCl2
10mM NaF
2mM AlCl3
0.05% octyl-beta-glucoside
cryo-EM vitrification conditions
Cryogen ETHANE；wait time of 5s, blot force at 3, and a blot time of 2s with Whatman blotting paper (Cytiva, CAT No. 10311807)
|
Resolution 2.80 Å |
| 8OOA CryoEM Structure INO80core Hexasome complex Hexasome refinement state1 Deposited 2023-04-04 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric |
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 7.5；30mM HEPES, pH7.5
50mM NaCl
0.25mM CaCl2
0.25mM DTT
2mM ADP
3.3mM MgCl2
10mM NaF
2mM AlCl3
0.05% octyl-beta-glucoside
cryo-EM vitrification conditions
Cryogen ETHANE；wait time of 5s, blot force at 3, and a blot time of 2s with Whatman blotting paper (Cytiva, CAT No. 10311807)
|
Resolution 3.18 Å |
| 8OOP CryoEM Structure INO80core Hexasome complex composite model state2 Deposited 2023-04-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric |
Chain M
2–136（135 aa）
Chain Q
2–136（135 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 7 MG MAGNESIUM ION × 2 ALF TETRAFLUOROALUMINATE ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；30mM HEPES, pH7.5
50mM NaCl
0.25mM CaCl2
0.25mM DTT
2mM ADP
3.3mM MgCl2
10mM NaF
2mM AlCl3
0.05% octyl-beta-glucoside
cryo-EM vitrification conditions
Cryogen ETHANE；wait time of 5s, blot force at 3, and a blot time of 2s with Whatman blotting paper (Cytiva, CAT No. 10311807)
|
Resolution 2.70 Å |
| 8OOS CryoEM Structure INO80core Hexasome complex ATPase-hexasome refinement state 2 Deposited 2023-04-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric |
Chain M
2–136（135 aa）
Chain Q
2–136（135 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ALF TETRAFLUOROALUMINATE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；30mM HEPES, pH7.5
50mM NaCl
0.25mM CaCl2
0.25mM DTT
2mM ADP
3.3mM MgCl2
10mM NaF
2mM AlCl3
0.05% octyl-beta-glucoside
cryo-EM vitrification conditions
Cryogen ETHANE；wait time of 5s, blot force at 3, and a blot time of 2s with Whatman blotting paper (Cytiva, CAT No. 10311807)
|
Resolution 3.29 Å |
| 8OSJ Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL-6.2 (DNA conformation 1) Deposited 2023-04-19 | Different construct Different mutation/modification Different oligomeric state 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 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.20 Å |
| 8OSK Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL+5.8 (composite map) Deposited 2023-04-19 | Different construct Different mutation/modification Different oligomeric state 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 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 8OSL Cryo-EM structure of CLOCK-BMAL1 bound to the native Por enhancer nucleosome (map 2, additional 3D classification and flexible refinement) Deposited 2023-04-19 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
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 4.90 Å |
| 8OTS OCT4 and MYC-MAX co-bound to a nucleosome Deposited 2023-04-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | PTD PENTANEDIAL × 8 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8OTT MYC-MAX bound to a nucleosome at SHL+5.8 Deposited 2023-04-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
40–134（95 aa）
Chain E
40–134（95 aa）
|
Not recorded | PTD PENTANEDIAL × 8 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8OX0 Structure of apo telomeric nucleosome Deposited 2023-04-28 | Different construct Different mutation/modification Different oligomeric state 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；25 mM HEPES-KOH pH 8.0, 150 mM KCl, 1 mM MgCl2, 1% glycerol, 0.01% Igepal CA-630,1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE；Blot Force: -15
Blot Time: 2.5 s
|
Resolution 2.52 Å |
| 8OX1 Structure of TRF1core in complex with telomeric nucleosome Deposited 2023-04-28 | Different construct Different mutation/modification Different oligomeric state 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 8；25 mM HEPES-KOH pH 8.0, 150 mM KCl, 1 mM MgCl2, 1% glycerol, 0.01% Igepal CA-630,
1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE；Blot Force: -15
Blot Time: 2.5 s
|
Resolution 2.70 Å |
| 8Q36 Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Foamy Virus GAG Peptide-Au[I] Compound) Deposited 2023-08-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain AAA
39–136（98 aa）
Chain EEE
39–136（98 aa）
|
Not recorded | MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0].
|
Resolution 2.60 Å R-free 0.262 |
| 8Q3E High Resolution Structure of Nucleosome Core with Bound Foamy Virus GAG Peptide Deposited 2023-08-04 | Different construct Different 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 AAA
39–136（98 aa）
Chain EEE
39–136（98 aa）
|
Not recorded | MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
|
Resolution 2.17 Å R-free 0.270 |
| 8Q3M Structure of Nucleosome Core with a Bound Kaposi Sarcoma Associated Herpesvirus LANA Peptide Having a Methionine to Ornithine Substitution Deposited 2023-08-04 | Different construct Different 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 AAA
39–136（98 aa）
Chain EEE
39–136（98 aa）
|
Not recorded | MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
|
Resolution 2.50 Å R-free 0.268 |
| 8Q3X Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Kaposi Sarcoma Associated Herpesvirus LANA Peptide-Au[I] Compound) Deposited 2023-08-04 | Different construct Different 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 AAA
39–136（98 aa）
Chain EEE
39–136（98 aa）
|
Not recorded | AU GOLD ION × 1 XIS 4-diphenylphosphanylbenzoic acid × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
|
Resolution 2.30 Å R-free 0.262 |
| 8QKT Structure of a nucleosome composed of a palindromic 167-base pair blunt-ended DNA fragment Deposited 2023-09-17 | 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 × 8 PDB declaration: decameric |
Chain AAA
39–136（98 aa）
Chain EEE
39–136（98 aa）
|
Not recorded | MN MANGANESE (II) ION × 19 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；MnCl2-containing buffers
|
Resolution 3.26 Å R-free 0.321 |
| 8QKT Structure of a nucleosome composed of a palindromic 167-base pair blunt-ended DNA fragment Deposited 2023-09-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain KKK
39–136（98 aa）
Chain OOO
39–136（98 aa）
|
Not recorded | MN MANGANESE (II) ION × 14 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；MnCl2-containing buffers
|
Resolution 3.26 Å R-free 0.321 |
| 8RGM Cryo-EM structure of nucleosome containing Widom603 DNA Deposited 2023-12-14 | Different construct Different mutation/modification Different oligomeric state 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 4.00 Å |
| 8SMW Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 1) Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8SMX Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 2) Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8SMY Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 3) Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8SMZ Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (Class 4) Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8SN0 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 5) Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8SN1 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 6) Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8SN2 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c (UbcH5c chemically conjugated to histone H2A) Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 8SN3 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 8SN4 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8SN5 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 3) Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 8SN6 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 4) Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8SN7 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 5) Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8SN8 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 6) Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8SN9 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 8SNA Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 8SPS High resolution structure of ESRRB nucleosome bound OCT4 at site a and site b Deposited 2023-05-03 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: tetradecameric |
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 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8SPU Structure of ESRRB nucleosome bound OCT4 at site c Deposited 2023-05-03 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 11 PDB declaration: tridecameric |
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 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8SWI Crystal structure of legAS4 from Legionella pneumophila subsp. pneumophila with histone H3 (1-12)peptide Deposited 2023-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–13（12 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1M Bis-Tris 6.5 and 38% PPG P400
|
Resolution 3.00 Å R-free 0.310 |
| 8SYP Genomic CX3CR1 nucleosome Deposited 2023-05-25 | Different construct Different mutation/modification Different oligomeric state 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 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 8TXV Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 1) Deposited 2023-08-24 | Different construct Different mutation/modification Different oligomeric state 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
|
Resolution 3.80 Å |
| 8TXW Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 2) Deposited 2023-08-24 | Different construct Different mutation/modification Different oligomeric state 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
|
Resolution 3.60 Å |
| 8TXX Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 3) Deposited 2023-08-24 | Different construct Different mutation/modification Different oligomeric state 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
|
Resolution 3.70 Å |
| 8U13 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 1) Deposited 2023-08-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 8U14 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 2) Deposited 2023-08-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 8U9S Cryo-EM structure of NRCAM nucleosome aided by scFv Deposited 2023-09-20 | Different construct Different mutation/modification Different oligomeric state 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
|
Resolution 2.60 Å |
| 8UBJ Cryo-EM structure of NRCAM nucleosome aided by scFv (3D Flex map) Deposited 2023-09-23 | Different construct Different mutation/modification Different oligomeric state 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
|
Resolution 2.80 Å |
| 8UBK Cryo-EM structure of Ascl1/E12a in complex with NRCAM nucleosome Deposited 2023-09-23 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric |
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 2.60 Å |
| 8UBL Cryo-EM structure of Ascl1/E12a in complex with NRCAM nucleosome (3D Flex map) Deposited 2023-09-23 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric |
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 2.80 Å |
| 8UPF Cryo-EM structure of the human nucleosome core particle in complex with RNF168-UbcH5c Deposited 2023-10-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8VFX Cryo-EM structure of 186bp ALBN1 nucleosome aided by scFv Deposited 2023-12-22 | Different construct Different mutation/modification Different oligomeric state 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
|
Resolution 2.65 Å |
| 8VFY Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 1) Deposited 2023-12-22 | Different construct Different mutation/modification Different oligomeric state 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
|
Resolution 2.89 Å |
| 8VFZ Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 2) Deposited 2023-12-22 | Different construct Different mutation/modification Different oligomeric state 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
|
Resolution 4.10 Å |
| 8VG0 Cryo-EM structure of GATA4 in complex with ALBN1 nucleosome Deposited 2023-12-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information 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 3.07 Å |
| 8VG1 Cryo-EM structure of FoxA1 and GATA4 in complex with ALBN1 nucleosome Deposited 2023-12-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric |
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 2.48 Å |
| 8VG2 Cryo-EM structure of FoxA1 and GATA4 in complex with H14 chromatosome Deposited 2023-12-22 | Different construct Different mutation/modification Different oligomeric state 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
|
Resolution 3.04 Å |
| 8VLR Cryo-EM structure of native H2AK119bu nucleosome at 2.6 Deposited 2024-01-12 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
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 7.5；20 mM Tris-HCl, pH 7.5, 50 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 8VMI PRC2_AJ119-450 bound to H3K4me3 Deposited 2024-01-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain B
2–7（6 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8VML PRC2_AJ1-450 bound to H3K4me3 Deposited 2024-01-13 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain I
20–41（22 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 8VNV PRC2_AJ1-450 bound to H3K36me3 with histone H3 tail engaged Deposited 2024-01-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric |
Chain I
20–41（22 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8W9D Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 1 Deposited 2023-09-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 7 K POTASSIUM ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 8W9E Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 2 Deposited 2023-09-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 7 K POTASSIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 8W9F Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 3 Deposited 2023-09-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.40 Å |
| 8WG5 Cryo-EM structure of USP16 bound to H2AK119Ub nucleosome Deposited 2023-09-20 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
38–135（98 aa）
Chain E
38–135（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 3.05 Å |
| 8X15 Structure of nucleosome-bound SRCAP-C in the apo state Deposited 2023-11-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric |
Chain C
1–136（136 aa）
Chain G
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8X19 Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state Deposited 2023-11-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric |
Chain C
1–136（136 aa）
Chain G
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 7 MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8X1C Structure of nucleosome-bound SRCAP-C in the ADP-bound state Deposited 2023-11-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric |
Chain C
1–136（136 aa）
Chain G
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 7 ATP ADENOSINE-5'-TRIPHOSPHATE × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8XBT The cryo-EM structure of the octameric RAD51 ring bound to the nucleosome with the linker DNA binding Deposited 2023-12-07 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-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 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.12 Å |
| 8XBU The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome with the linker DNA binding Deposited 2023-12-07 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-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 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.24 Å |
| 8XBW The cryo-EM structure of the RAD51 N-terminal lobe domain bound to the histone H4 tail of the nucleosome Deposited 2023-12-07 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric |
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 2.89 Å |
| 8XRJ RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei Deposited 2024-01-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric |
Chain a
2–136（135 aa）
Chain e
2–136（135 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 8XVS RNA polymerase II elongation complex with downstream nucleosome extracted from human nuclei Deposited 2024-01-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric |
Chain a
2–136（135 aa）
Chain e
2–136（135 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 8Y3C Cryo-EM structure of the overlapping di-nucleosome (closed form) Deposited 2024-01-29 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric |
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 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.21 Å |
| 8Y3D Cryo-EM structure of the overlapping di-nucleosome (intermediate form2) Deposited 2024-01-29 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric |
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 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.10 Å |
| 8Y3E Cryo-EM structure of the overlapping di-nucleosome (open form) Deposited 2024-01-29 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-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）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.32 Å |
| 8Y3F Cryo-EM structure of the overlapping di-nucleosome (intermediate form1) Deposited 2024-01-29 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric |
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 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.54 Å |
| 8YBJ Cryo-EM structure of human nucleosome core particle composed of the Widom 601 DNA sequence Deposited 2024-02-14 | Different construct Different mutation/modification Different oligomeric state 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-PROPANE
|
Resolution 2.38 Å |
| 8YBK Cryo-EM structure of the human nucleosome containing the H3.1 E97K mutant Deposited 2024-02-14 | Different construct Different mutation/modification Different oligomeric state 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：E97K Mutation：E97K | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 2.69 Å |
| 8YJF Structure of human SPT16 MD-CTD and MCM2 HBD chaperoning a histone H3-H4 tetramer and an H2A-H2B dimer Deposited 2024-03-01 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain C
57–136（80 aa）
Chain E
57–136（80 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；0.1 M calcium acetate, 0.1 M Sodium cacodylate pH 5.5, 12% (w/v) PEG 8000
|
Resolution 4.40 Å R-free 0.312 |
| 8YJM Structure of human SPT16 MD-CTD and MCM2 HBD chaperoning a histone H3-H4 tetramer and a single chain H2B-H2A chimera Deposited 2024-03-02 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric |
Chain C
57–136（80 aa）
Chain E
57–136（80 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；0.2 M sodium acetate, 0.1 M sodium citrate pH 5.5, 5%(w/v) PEG 4000
|
Resolution 4.15 Å R-free 0.286 |
| 8YNY Structure of Cas9-sgRNA ribonucleoprotein bound to nucleosome Deposited 2024-03-12 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: 13-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 4.52 Å |
| 8YTI Crystal Structure of Nucleosome-H1x Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2024-03-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric |
Chain 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 | CL CHLORIDE ION × 8 CA CALCIUM ION × 52 K POTASSIUM ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；40-45 mM CaCl2, 25 mM KCl, 10 mM Na-acetate (pH 4.5)
|
Resolution 2.70 Å R-free 0.267 |
| 8YV8 Cryo-EM structure of CDCA7 bound to nucleosome including hemimethylated CpG site in Widom601 positioning sequence. Deposited 2024-03-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 9ECP Structure of the native human NCP purified from HEK293 cells Deposited 2024-11-14 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
39–134（96 aa）
Chain E
39–134（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 1.91 Å |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain Q
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 10 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain Z
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 11 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain a
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 12 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain b
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 13 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain c
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 14 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain d
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 15 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain e
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 16 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain f
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain R
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain S
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain T
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain U
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain V
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain W
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain X
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 9 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain Y
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9FGQ Structure of human APC3loop 375-381 bound to the NCP Deposited 2024-05-24 | Different construct Different mutation/modification Different oligomeric state 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 8；20 mM HEPEs pH8.0, 50 mM NaCl, 0.5 mM TCEP
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å |
| 9FH9 Structure of CyclinB1 N-terminus bound to the NCP Deposited 2024-05-27 | Different construct Different mutation/modification Different oligomeric state 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 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å |
| 9GCG CryoEM structure of the human INO80 core- H2A.Z nucleosome complex Deposited 2024-08-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric |
Chain M
1–136（136 aa）
Chain Q
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 7 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.43 Å |
| 9GE4 CryoEM structure of the human INO80 core- H2A.Z nucleosome complex Deposited 2024-08-07 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain M
1–136（136 aa）
Chain Q
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 3.52 Å |
| 9GE5 CryoEM structure of the human INO80-Hexasome complex Deposited 2024-08-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric |
Chain M
43–136（94 aa）
Chain Q
43–136（94 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.35 Å |
| 9GEL CryoEM structure of the human INO80-Hexasome complex Deposited 2024-08-07 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric |
Chain M
1–136（136 aa）
Chain Q
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 4.86 Å |
| 9GEV CryoEM structure of the human INO80 core-nucleosome complex state N-6 Deposited 2024-08-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric |
Chain M
1–136（136 aa）
Chain Q
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.47 Å |
| 9GF6 CryoEM structure of the human INO80 core-nucleosome complex state N-6 Deposited 2024-08-08 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
Chain M
1–136（136 aa）
Chain Q
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 3.80 Å |
| 9GFB CryoEM structure of the human INO80 core-nucleosome complex state N-7 Deposited 2024-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric |
Chain M
1–136（136 aa）
Chain Q
1–136（136 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 6 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.55 Å |
| 9GFM CryoEM structure of the human INO80 core-nucleosome complex state N-7 Deposited 2024-08-09 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
Chain M
44–136（93 aa）
Chain Q
37–136（100 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 9IGW Ku70/80 bound to 147 bp nucleosome Deposited 2025-02-20 | Different construct Different mutation/modification Different oligomeric state 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 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.32 Å |
| 9IGX Ku70/80 bound to 153 bp nucleosome Deposited 2025-02-20 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric |
Chain A
39–135（97 aa）
Chain E
39–135（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 3.56 Å |
| 9J8M Cryo-EM structure of BAF-Lamin A/C IgF-nucleosome complex (High mobility complex) Deposited 2024-08-21 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
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 3.82 Å |
| 9J8N Cryo-EM structure of BAF-Lamin A/C IgF-nucleosome complex (Low mobility complex) Deposited 2024-08-21 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 32-meric |
Chain A
1–136（136 aa）
Chain E
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 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.14 Å |
| 9J8O Cryo-EM structure of BAF-Lamin A/C IgF-H1-nucleosome complex Deposited 2024-08-21 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 28-meric |
Chain A
1–136（136 aa）
Chain E
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 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.05 Å |
| 9J8W Cryo-EM structure of NCP-UV-DDB complex containing CPD Deposited 2024-08-21 | Different construct Different mutation/modification Different oligomeric state 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 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.38 Å |
| 9JC6 Human H2BW2 nucleosome Deposited 2024-08-28 | Different construct Different mutation/modification Different oligomeric state 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 3.34 Å |
| 9MLL GammaH2AX containing nucleosomes, Parallel stack Deposited 2024-12-19 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
Chain L
1–136（136 aa）
Chain P
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 3.70 Å |
| 9MLN GammaH2AX containing nucleosome, Canonical (Class 1) Deposited 2024-12-19 | Different construct Different mutation/modification Different oligomeric state 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 3.30 Å |
| 9MLR GammaH2AX containing nucleosome, Half-wrapped (Class 2) Deposited 2024-12-19 | Different construct Different mutation/modification Different oligomeric state 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 3.10 Å |
| 9MLS GammaH2AX containing nucleosome, Extended (Class 3) Deposited 2024-12-19 | Different construct Different mutation/modification Different oligomeric state 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 3.60 Å |
| 9MMK H2AX containing nucleosome, Canonical (Class 1) Deposited 2024-12-20 | Different construct Different mutation/modification Different oligomeric state 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 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9MMM H2AX containing nucleosomes, Parallel stack Deposited 2024-12-20 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
Chain L
1–136（136 aa）
Chain P
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 9MMN H2AX containing nucleosomes, Left offset stack Deposited 2024-12-20 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
Chain L
1–136（136 aa）
Chain P
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 9MMO H2AX containing nucleosomes, Right offset stack Deposited 2024-12-20 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
Chain L
1–136（136 aa）
Chain P
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 9MMT H2AX containing nucleosome, Unwrapped (Class 2) Deposited 2024-12-20 | Different construct Different mutation/modification Different oligomeric state 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 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 9Q80 Ku70/80 with Ku70 linker and SAP domain bound to a 153 bp H2AX nucleosome Deposited 2025-02-21 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-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 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.39 Å |
| 9Q8X Ku70/80 bound to a 153 bp H2AX nucleosome Deposited 2025-02-25 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-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 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.94 Å |
| 9Q9F DNA-PK bound to a 153 bp H2AX nucleosome model 1 Deposited 2025-02-26 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-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 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.54 Å |
| 9QCR DNA-PK bound to 153 bp H2AX nucleosome model 2 Deposited 2025-03-05 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-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 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.37 Å |
| 9QCS Ku80 mediated DNA-PK dimer bound to 153 bp H2AX nucleosome Deposited 2025-03-05 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 26-meric |
Chain A
1–136（136 aa）
Chain E
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 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.38 Å |
| 9QLM Solution structure of the TAF3-PHD bound to a H3K4me3Q5ser histone tail peptide with a serotonylated glutamine 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 heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–13（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 SRO SEROTONIN × 1 |
SOLUTION NMR
NMR measurement conditions
pH 7；293 K；Ionic strength (raw mmCIF value) 44；Pressure 1
NMR sample composition
0.88 mM [U-13C; U-15N] TAF3-PHD, 0.88 mM H3K4me3Q5ser, 20 mM potassium phosphate, 4 mM potassium chloride, 10 uM zinc chloride, 0.01 % w/v sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 9QMS DNA-PK bound to 153 bp H2AX nucleosome with ATPyS Deposited 2025-03-24 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 30-meric |
Chain A
1–136（136 aa）
Chain E
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 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.00 Å |
| 9R04 p53 bound to the nucleosome at position SHL-5.7 (crosslinked sample) Deposited 2025-04-24 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-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 4.20 Å |
| 9R2M p53 bound to nucleosome at position SHL+5.9 (non-crosslinked sample, composite map) Deposited 2025-04-30 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-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 |
| 9R2P p53 bound to nucleosome at position SHL+5.9 (crosslinked sample) Deposited 2025-04-30 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-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 4.18 Å |
| 9R2Q p53 bound to nucleosome at position SHL-5.7 (non-crosslinked sample) Deposited 2025-04-30 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-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 3.20 Å |
| 9RL4 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL-6 Deposited 2025-06-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | PTD PENTANEDIAL × 16 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 9RMC Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 1 Deposited 2025-06-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 9RN1 Structure of BAF-nucleosome complex with OCT4-SOX2 at SHL+6 in ADP-bound state, BAF47 bound to ATPase lobe 2 Deposited 2025-06-19 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-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 5.90 Å |
| 9RN2 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 2 Deposited 2025-06-19 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 19 PDB declaration: 21-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 4.10 Å |
| 9UJS RNA polymerase II elongation complex stalled at SHL(-4) of the H3-H4 octasome Deposited 2025-04-17 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric |
Chain a
1–136（136 aa）
Chain c
1–136（136 aa）
Chain e
1–136（136 aa）
Chain g
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 3.62 Å |
| 9UJT RNA polymerase II elongation complex stalled at SHL(-0.5) of the H3-H4 octasome (tetrasome) Deposited 2025-04-17 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric |
Chain e
1–136（136 aa）
Chain g
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 6.54 Å |
| 9UZ7 Cryo-EM structure of the nucleosome core particle with site-specific DNA-histone crosslinking Deposited 2025-05-16 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain B
2–136（135 aa）
|
Mutation：C96S/C110S/K115C Mutation：C96S/C110S/K115C Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6；10 mM HEPES, pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution not provided |
| 9V6Q Cryo-EM structure of two cPRC1 complexes bound to opposite faces of an endogenous 147-bp mono-nucleosome Deposited 2025-05-27 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 4.60 Å |
| 9V6S Cryo-EM structure of a single cPRC1 complex engaged on one face of an endogenous 147-bp mononucleosome Deposited 2025-05-27 | Different construct Different mutation/modification Different oligomeric state 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 mmCIF provides none of the parsed conditions | Resolution 3.00 Å |
| 9V6X Cryo-EM structure of the cPRC1 complex bound to an endogenous 184-bp mono-nucleosome Deposited 2025-05-27 | Different construct Different mutation/modification Different oligomeric state 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 mmCIF provides none of the parsed conditions | Resolution 4.00 Å |
| 9V8L Cryo-EM structure of the cPRC1-di-nucleosome (loose) complex Deposited 2025-05-29 | Different construct Different mutation/modification Different oligomeric state Different 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 mmCIF provides none of the parsed conditions | Resolution 6.60 Å |
| 9V9H Cryo-EM structure of the cPRC1-di-nucleosome (tight) complex Deposited 2025-05-30 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
Chain K
1–136（136 aa）
Chain M
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 4.50 Å |
| 9V9P Cryo-EM structure of the cPRC1-di-nucleosome (CBX7) complex Deposited 2025-06-01 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
Chain K
1–136（136 aa）
Chain M
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.40 Å |
| 9VEM SIRT2 structure in complex with H3K18myr peptide and native NAD: pre-catalysis state 1 Deposited 2025-06-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
17–22（6 aa）
|
Not recorded | NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 PEG DI(HYDROXYETHYL)ETHER × 2 EDO 1,2-ETHANEDIOL × 5 GOL GLYCEROL × 1 ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；Tris 8.0, 25% PEG 2000MME
|
Resolution 2.57 Å R-free 0.264 |
| 9VEW SIRT2 structure in complex with H3K18myr peptide and native NAD: pre-catalysis state 2 Deposited 2025-06-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
16–22（7 aa）
|
Not recorded | NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 1 ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；Tris 8.0, 25% PEG 2000MME
|
Resolution 2.68 Å R-free 0.251 |
| 9VG0 SIRT2 structure in complex with H3K18myr peptide Deposited 2025-06-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
16–22（7 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 5 ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；Tris 8.0, 25% PEG 2000MME
|
Resolution 1.61 Å R-free 0.231 |
| 9VG3 SIRT2 structure in complex with H3K18myr peptide: pre NAD binding state Deposited 2025-06-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
17–22（6 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 2 ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；Tris 8.0, 25% PEG2000MME
|
Resolution 2.15 Å R-free 0.251 |
| 9VGE SIRT2 demyristoylation intermediate I structure Deposited 2025-06-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
16–22（7 aa）
|
Not recorded | NCA NICOTINAMIDE × 1 GOL GLYCEROL × 1 ZN ZINC ION × 1 YDD [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5S)-3,4-bis(oxidanyl)-5-tetradecoxy-oxolan-2-yl]methyl hydrogen phosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；Tris 8.0, 25% PEG 2000MME
|
Resolution 2.56 Å R-free 0.282 |
| 9VGZ SIRT2-F96A structure in complex with H3K18myr peptide and native NAD Deposited 2025-06-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
16–22（7 aa）
|
Not recorded | NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；Tris 8.0, 25% PEG 2000MME
|
Resolution 2.34 Å R-free 0.236 |
| 9VH0 SIRT2-H187A structure in complex with H3K18myr peptide and native NAD Deposited 2025-06-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
16–21（6 aa）
|
Not recorded | NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；0.1 M MES 5.5, 9.2% PEG10000
|
Resolution 2.41 Å R-free 0.273 |
| 9VH0 SIRT2-H187A structure in complex with H3K18myr peptide and native NAD Deposited 2025-06-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
16–21（6 aa）
|
Not recorded | NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；0.1 M MES 5.5, 9.2% PEG10000
|
Resolution 2.41 Å R-free 0.273 |
| 9XSF Cryo-EM structure of H4S47GlcNAc nucleosome at 3.39 angstrom Deposited 2025-11-20 | Different construct Different mutation/modification Different oligomeric state 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 mmCIF provides none of the parsed conditions | Resolution 3.39 Å |
| 9YL3 State 1 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.50 Å |
| 9YLE State 3 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.63 Å |
| 9YLY MLL4FC bound to a nucleosome with p53 RE Deposited 2025-10-09 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 14 PDB declaration: 16-meric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.77 Å |
| 9YM8 State 2 focused on PHD FYR of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.43 Å |
| 9YMF State 2 focused on H3 N terminal tail of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.45 Å |
| 9ZEO Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1G1 Deposited 2025-11-30 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
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；20 mM HEPES pH7.6, 50 mM NaCl, 0.5 mM MgCl2, 1 mM EDTA
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
402 other PDB entries and 475 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | H31_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–136； UniProt 1–136 Author chain E； PDBConstruct 1–136； UniProt 1–136 Author chain K； PDBConstruct 1–136； UniProt 1–136 Author chain O； PDBConstruct 1–136； UniProt 1–136 Author chain S； PDBConstruct 1–136； UniProt 1–136 Author chain W； PDBConstruct 1–136； UniProt 1–136 |
