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8hqy

Cryo-EM structure of SSX1 bound to the H2AK119Ub nucleosome at a resolution of 3.05 angstrom

Method: ELECTRON MICROSCOPY Dmax: 121.7 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone H3

Homo sapiens

UniProt A0A653DHJ5

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 10 DNA 2 PDB declaration: dodecameric（12） Consistent with all polymer counts Chain A； UniProt 39–135 Chain E； UniProt 39–135 Not recorded Histone H4 (Fragment) × 1 （A0A093PN76） Histone H2A type 1-B/E × 1 （P04908） Histone H2B type 1-K × 2 （O60814） Histone H4 × 1 （A0A8C2GGI7） Histone H2A type 1-B/E × 1 （P04908） Protein SSX2 × 1 （Q16385） Polyubiquitin-B (Fragment) × 1 （J3QS39） DNA (137-MER) × 1 DNA (136-MER) × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.05 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 8HQY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8GRQ Cryo-EM structure of BRCA1/BARD1 bound to H2AK127-UbcH5c-Ub nucleosome Deposited 2022-09-02 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 38–135（98 aa）
Chain E 38–135（98 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.87 Å
8HR1 Cryo-EM structure of SSX1 bound to the unmodified nucleosome at a resolution of 3.02 angstrom Deposited 2022-12-14 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-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 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.02 Å
8UX1 Cryo-EM structure of Ran bound to RCC1 and the nucleosome core particle Deposited 2023-11-08 Different construct Different mutation/modification 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）
Mutation：C110S Mutation：C110S No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
9KQO cryo-EM structure of RNF20/RNF40-RAD6A-Ub in complex with H2BS112GlcNAc nucleosome Deposited 2024-11-26 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain E 2–136（135 aa）
Chain K 2–136（135 aa）
Not recorded ZN ZINC ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.48 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A653DHJ5_CALMS
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–97； UniProt 39–135 Author chain E； PDBConstruct 1–97； UniProt 39–135

Histone H4 (Fragment)

Homo sapiens

UniProt A0A093PN76

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 10 DNA 2 PDB declaration: dodecameric（12） Consistent with all polymer counts Chain B； UniProt 1–83 Not recorded Histone H3 × 2 （A0A653DHJ5） Histone H2A type 1-B/E × 1 （P04908） Histone H2B type 1-K × 2 （O60814） Histone H4 × 1 （A0A8C2GGI7） Histone H2A type 1-B/E × 1 （P04908） Protein SSX2 × 1 （Q16385） Polyubiquitin-B (Fragment) × 1 （J3QS39） DNA (137-MER) × 1 DNA (136-MER) × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.05 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name A0A093PN76_9PASS
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–83； UniProt 1–83

Histone H2A type 1-B/E

Homo sapiens

UniProt P04908

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 10 DNA 2 PDB declaration: dodecameric（12） Consistent with all polymer counts Chain C； UniProt 14–119 Chain G； UniProt 14–119 Not recorded Histone H3 × 2 （A0A653DHJ5） Histone H4 (Fragment) × 1 （A0A093PN76） Histone H2B type 1-K × 2 （O60814） Histone H4 × 1 （A0A8C2GGI7） Protein SSX2 × 1 （Q16385） Polyubiquitin-B (Fragment) × 1 （J3QS39） DNA (137-MER) × 1 DNA (136-MER) × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.05 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 8HQY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2RVQ Solution structure of the isolated histone H2A-H2B heterodimer Deposited 2016-03-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–130（130 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；293 K；Ionic strength (raw mmCIF value) 400；Pressure ambient
NMR sample composition 0.1-0.3 mM [U-13C; U-15N; U-2H] entity_1-1, 0.1-0.3 mM [U-13C; U-15N; U-2H] entity_2-2, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
3A6N The nucleosome containing a testis-specific histone variant, human H3T Deposited 2009-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.70 Å R-free 0.264
3AFA The human nucleosome structure Deposited 2010-02-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.270
3AN2 The structure of the centromeric nucleosome containing CENP-A Deposited 2010-08-27 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.60 Å R-free 0.325
3AV1 The human nucleosome structure containing the histone variant H3.2 Deposited 2011-02-18 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.290
3AV2 The human nucleosome structure containing the histone variant H3.3 Deposited 2011-02-18 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.272
3AYW Crystal Structure of Human Nucleosome Core Particle Containing H3K56Q mutation Deposited 2011-05-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.90 Å R-free 0.273
3AZE Crystal Structure of Human Nucleosome Core Particle Containing H3K64Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.00 Å R-free 0.302
3AZF Crystal Structure of Human Nucleosome Core Particle Containing H3K79Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.70 Å R-free 0.263
3AZG Crystal Structure of Human Nucleosome Core Particle Containing H3K115Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.40 Å R-free 0.269
3AZH Crystal Structure of Human Nucleosome Core Particle Containing H3K122Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 3 MN MANGANESE (II) ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.49 Å R-free 0.266
3AZI Crystal Structure of Human Nucleosome Core Particle Containing H4K31Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.70 Å R-free 0.289
3AZJ Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.89 Å R-free 0.268
3AZK Crystal Structure of Human Nucleosome Core Particle Containing H4K59Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.20 Å R-free 0.258
3AZL Crystal Structure of Human Nucleosome Core Particle Containing H4K77Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.70 Å R-free 0.259
3AZM Crystal Structure of Human Nucleosome Core Particle Containing H4K79Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 3 MN MANGANESE (II) ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.89 Å R-free 0.296
3AZN Crystal Structure of Human Nucleosome Core Particle Containing H4K91Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.00 Å R-free 0.254
3W96 Crystal Structure of Human Nucleosome Core Particle lacking H2A N-terminal region Deposited 2013-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 11–130（120 aa） Fragment：UNP residues 11-130
Chain G 11–130（120 aa） Fragment：UNP residues 11-130
Not recorded CL CHLORIDE ION × 1 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.00 Å R-free 0.296
3W97 Crystal Structure of Human Nucleosome Core Particle lacking H2B N-terminal region Deposited 2013-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.20 Å R-free 0.321
3W98 Crystal Structure of Human Nucleosome Core Particle lacking H3.1 N-terminal region Deposited 2013-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.42 Å R-free 0.303
3W99 Crystal Structure of Human Nucleosome Core Particle lacking H4 N-terminal region Deposited 2013-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.00 Å R-free 0.312
3WKJ The nucleosome containing human TSH2B Deposited 2013-10-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.291
3WTP Crystal Structure of the heterotypic nucleosome containing human CENP-A and H3.3 Deposited 2014-04-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, vapor diffusion, hanging drop, temperature 293K
Resolution 2.67 Å R-free 0.270
3X1S Crystal structure of the nucleosome core particle Deposited 2014-11-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded MN MANGANESE (II) ION × 6 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；60-70mM KCL, 70-90mM MnCl2, 24% MPD, 20mM Na-Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.81 Å R-free 0.270
3X1V Crystal structure of nucleosome core particle in the presence of histone variant involved in reprogramming Deposited 2014-11-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded MN MANGANESE (II) ION × 19 CL CHLORIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；60-70 mM KCl, 70-90 mM MnCl2, Na-cocodylate, 24% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.92 Å R-free 0.259
4YM5 Crystal structure of the human nucleosome containing 6-4PP (inside) Deposited 2015-03-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 4.00 Å R-free 0.289
4YM6 Crystal structure of the human nucleosome containing 6-4PP (outside) Deposited 2015-03-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 3.51 Å R-free 0.287
4Z5T The nucleosome containing human H3.5 Deposited 2015-04-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.80 Å R-free 0.269
5AV5 human nucleosome core particle Deposited 2015-06-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions LIQUID DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.40 Å R-free 0.233
5AV6 human nucleosome core particle Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.20 Å R-free 0.229
5AV8 human nucleosome core particle Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.20 Å R-free 0.233
5AV9 human nucleosome core particle Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.20 Å R-free 0.239
5AVB human nucleosome core particle Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.40 Å R-free 0.236
5AVC human nucleosome core particle Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.40 Å R-free 0.238
5AY8 Crystal structure of human nucleosome containing H3.Y Deposited 2015-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 8 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；sodium acetate, manganese chloride, 2-propanol, trimethylamine N-oxide
Resolution 2.80 Å R-free 0.249
5B0Y Crystal structure of the nucleosome containing histone H3 with the crotonylated lysine 122 Deposited 2015-11-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.56 Å R-free 0.249
5B0Z The crystal structure of the nucleosome containing H3.2, at 1.98 A resolution Deposited 2015-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 1.99 Å R-free 0.254
5B24 The crystal structure of the nucleosome containing cyclobutane pyrimidine dimer Deposited 2015-12-31 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 3.60 Å R-free 0.249
5B2I Human nucleosome containing CpG unmethylated DNA Deposited 2016-01-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 3.00 Å R-free 0.257
5B2J Human nucleosome containing CpG methylated DNA Deposited 2016-01-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.60 Å R-free 0.252
5B31 The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.1. Deposited 2016-02-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 8 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.20 Å R-free 0.271
5B32 The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.3. Deposited 2016-02-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.35 Å R-free 0.259
5B40 The nucleosome structure containing H2B-K120 and H4-K31 monoubiquitinations Deposited 2016-03-22 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；90mM Tris-HCl (pH 7.8), 3.6% PGA-LM, 25.2% PEG 400, 2-6% Pentaerythritol ethoxylate (3/4 EO/OH)
Resolution 3.33 Å R-free 0.263
5CPI Nucleosome containing unmethylated Sat2R DNA Deposited 2015-07-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.90 Å R-free 0.295
5CPJ Nucleosome containing methylated Sat2R DNA Deposited 2015-07-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 3.15 Å R-free 0.295
5CPK Nucleosome containing methylated Sat2L DNA Deposited 2015-07-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.63 Å R-free 0.284
5GSE Crystal structure of unusual nucleosome Deposited 2016-08-16 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；potassium bromide, potassium thiocyanate, Tris-HCl, PGA-LM, PEG 400
Resolution 3.14 Å R-free 0.255
5GTC Crystal structure of complex between DMAP-SH conjugated with a Kaposi's sarcoma herpesvirus LANA peptide (5-15) and nucleosome core particle Deposited 2016-08-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.70 Å R-free 0.267
5GXQ The crystal structure of the nucleosome containing H3.6 Deposited 2016-09-19 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.85 Å R-free 0.262
5JRG Crystal structure of the nucleosome containing the DNA with tetrahydrofuran (THF) Deposited 2016-05-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.50 Å R-free 0.245
5VEY Solution NMR structure of histone H2A-H2B mono-ubiquitylated at H2A Lys15 in complex with RNF169 (653-708) Deposited 2017-04-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 13–106（94 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 50 mM KCl；Pressure 1
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 50 mM KCl；Pressure 1
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
Resolution not provided
5X7X The crystal structure of the nucleosome containing H3.3 at 2.18 angstrom resolution Deposited 2017-02-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.18 Å R-free 0.256
5XF3 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,R-configuration) Deposited 2017-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 1 RUD [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 × 2 RRK (1R,2R)-1,2-diphenylethane-1,2-diamine × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；35-55 mM MnCl2, 25-49 mM KCl, 20 mM K-Cacodylate pH 6.0
Resolution 2.60 Å R-free 0.270
5XF4 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (S,S-configuration) Deposited 2017-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 1 RUD [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 × 2 SSK (1S,2S)-1,2-diphenylethane-1,2-diamine × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；35-55 mM MnCl2, 25-49 mM KCl, 20 mM K-Cacodylate pH 6.0
Resolution 2.87 Å R-free 0.266
5XF5 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,S-configuration) Deposited 2017-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 1 RUD [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 × 2 RSK (1S,2R)-1,2-diphenylethane-1,2-diamine × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；35-55mM MnCl2, 25-49mM KCl, 20mM K-Cacodylate pH 6.0
Resolution 2.82 Å R-free 0.264
5Y0C Crystal Structure of the human nucleosome at 2.09 angstrom resolution Deposited 2017-07-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 10 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.09 Å R-free 0.249
5Y0D Crystal Structure of the human nucleosome containing the H2B E76K mutant Deposited 2017-07-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 1.99 Å R-free 0.252
5Z23 Crystal structure of the nucleosome containing a chimeric histone H3/CENP-A CATD Deposited 2017-12-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Mutation：L51M,L58M,L93M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L51M,L58M,L93M Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.73 Å R-free 0.261
5ZBX The crystal structure of the nucleosome containing histone H3.1 CATD(V76Q, K77D) Deposited 2018-02-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.58 Å R-free 0.249
6A5L RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA Deposited 2018-06-24 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.60 Å
6A5O RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome Deposited 2018-06-25 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.90 Å
6A5P RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome Deposited 2018-06-25 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å
6A5R RNA polymerase II elongation complex stalled at SHL(-2) of the nucleosome Deposited 2018-06-25 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
6A5T RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome Deposited 2018-06-25 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.70 Å
6A5U RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation Deposited 2018-06-25 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
6BUZ Cryo-EM structure of CENP-A nucleosome in complex with kinetochore protein CENP-N Deposited 2017-12-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.92 Å
6E0C Cryo-EM structure of the CENP-A nucleosome (W601) in complex with a single chain antibody fragment Deposited 2018-07-06 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.63 Å
6E0P Cryo-EM structure of the centromeric nucleosome (Native alpha satellite DNA) in complex with a single chain antibody fragment Deposited 2018-07-06 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；blot for 2.5 sec before plunging
Resolution 2.60 Å
6HKT Structure of an H1-bound 6-nucleosome array Deposited 2018-09-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 48 PDB declaration: 50-meric
Chain 0 1–130（130 aa）
Chain 2 1–130（130 aa）
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain W 1–130（130 aa）
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Chain m 1–130（130 aa）
Chain q 1–130（130 aa）
Chain w 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；293.15 K；15% MPD, 0.1 M NaCl and 0.1 M Tris pH 8.8
Resolution 9.70 Å R-free 0.286
6HTS Cryo-EM structure of the human INO80 complex bound to nucleosome Deposited 2018-10-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain K 1–130（130 aa）
Chain O 1–130（130 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
6INQ RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position) Deposited 2018-10-26 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
6IPU Human nucleosome core particle containing 145 bp of DNA Deposited 2018-11-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 14–120（107 aa）
Chain G 14–120（107 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；manganese chloride, potassium chloride, potassium cacodylate
Resolution 1.99 Å R-free 0.263
6IQ4 Nucleosome core particle cross-linked with a hetero-binuclear molecule possessing RAPTA and gold(I) 4-(diphenylphosphino)benzoic acid groups. Deposited 2018-11-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 15–120（106 aa）
Chain G 15–120（106 aa）
Not recorded AU GOLD ION × 1 XIS 4-diphenylphosphanylbenzoic acid × 1 MG MAGNESIUM ION × 4 D0X [Ru(eta(6)-p-cymene)Cl-2(pta) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；manganese chloride, potassium chloride, potassium cacodylate
Resolution 2.25 Å R-free 0.257
6IR9 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome Deposited 2018-11-12 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6J4W RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-5) of the nucleosome Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.90 Å
6J4X RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1A) Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Y RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1B) Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Z RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6J50 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome (tilted conformation) Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
6J51 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome, weak Elf1 (+1 position) Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6JR0 Crystal structure of the human nucleosome phased with 12 selenium atoms Deposited 2019-04-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Mutation：L65M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L65M Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.50 Å R-free 0.253
6JR1 Crystal structure of the human nucleosome phased with 16 selenium atoms Deposited 2019-04-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Mutation：L65M, L85M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L65M, L85M Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.40 Å R-free 0.243
6JXD Human nucleosome core particle with cohesive end DNA termini Deposited 2019-04-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 14–119（106 aa）
Chain G 14–119（106 aa）
Not recorded MN MANGANESE (II) ION × 17 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；manganese chloride, potassium chloride, potassium cacodylate
Resolution 2.25 Å R-free 0.292
6KE9 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-07-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 15–119（105 aa）
Chain G 15–119（105 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
Resolution 2.22 Å R-free 0.230
6KXV Crystal structure of a nucleosome containing Leishmania histone H3 Deposited 2019-09-13 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；sodium acetate, isopropanol, manganese chloride, trimethylamine N-oxide
Resolution 3.63 Å R-free 0.264
6L49 H3-CA-H3 tri-nucleosome with the 22 base-pair linker DNA Deposited 2019-10-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain U 1–130（130 aa）
Chain Y 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 18.90 Å
6L4A H3-H3-H3 tri-nucleosome with the 22 base-pair linker DNA Deposited 2019-10-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain U 1–130（130 aa）
Chain Y 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 12.30 Å
6L9H The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-11-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 15–119（105 aa）
Chain G 15–119（105 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
Resolution 2.60 Å R-free 0.278
6L9Z 338 bp di-nucleosome assembled with linker histone H1.X Deposited 2019-11-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CL CHLORIDE ION × 8 CA CALCIUM ION × 65 K POTASSIUM ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；Calcium chloride, Potassium chloride, Potassium Cacodylate
Resolution 2.50 Å R-free 0.256
6LA2 343 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 Deposited 2019-11-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 34 PDB declaration: 38-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain W 1–130（130 aa）
Chain a 1–130（130 aa）
Chain g 1–130（130 aa）
Chain k 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, Potassium chloride, Sodium acetate
Resolution 3.89 Å R-free 0.267
6LA8 349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 Deposited 2019-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CA CALCIUM ION × 23 K POTASSIUM ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate (cryo-25% MPD)
Resolution 3.40 Å R-free 0.265
6LA9 349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 (high cryoprotectant) Deposited 2019-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CA CALCIUM ION × 40 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
Resolution 3.70 Å R-free 0.266
6LAB 169 bp nucleosome, harboring cohesive DNA termini, assembled with linker histone H1.0 Deposited 2019-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CA CALCIUM ION × 20 K POTASSIUM ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
Resolution 3.20 Å R-free 0.262
6LE9 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-11-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 15–119（105 aa）
Chain G 15–119（105 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
Resolution 2.60 Å R-free 0.281
6LER 169 bp nucleosome harboring non-identical cohesive DNA termini. Deposited 2019-11-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CA CALCIUM ION × 6 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
Resolution 3.00 Å R-free 0.261
6LER 169 bp nucleosome harboring non-identical cohesive DNA termini. Deposited 2019-11-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CA CALCIUM ION × 8 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
Resolution 3.00 Å R-free 0.261
6M3V 355 bp di-nucleosome harboring cohesive DNA termini Deposited 2020-03-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded K POTASSIUM ION × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；291 K；Calcium chloride, Potassium chloride, Potassium Cacodylate, Poly glutamic acid
Resolution 4.60 Å R-free 0.261
6M44 355 bp di-nucleosome harboring cohesive DNA termini (high cryoprotectant) Deposited 2020-03-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；Calcium chloride, Potassium chloride, Potassium Cacodylate, Poly glutamic acid
Resolution 3.81 Å R-free 0.286
6O1D Cryo-EM structure of the centromeric nucleosome with native alpha satellite DNA Deposited 2019-02-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；blot for 2.5 sec before plunging
Resolution 3.40 Å
6R8Y Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB Deposited 2019-04-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6R8Z Cryo-EM structure of NCP_THF2(-1)-UV-DDB Deposited 2019-04-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6R90 Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A Deposited 2019-04-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6R91 Cryo-EM structure of NCP_THF2(-3)-UV-DDB Deposited 2019-04-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6R92 Cryo-EM structure of NCP-THF2(+1)-UV-DDB class B Deposited 2019-04-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
6R93 Cryo-EM structure of NCP-6-4PP Deposited 2019-04-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6R94 Cryo-EM structure of NCP_THF2(-3) Deposited 2019-04-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6T79 Structure of a human nucleosome at 3.2 A resolution Deposited 2019-10-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 3.20 Å
6T7A Structure of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 3.70 Å
6T7B Structure of human Sox2 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 5.10 Å
6T7C Structure of two copies of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 4.00 Å
6T7D Structure of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 4.40 Å
6T90 OCT4-SOX2-bound nucleosome - SHL-6 Deposited 2019-10-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded PTD PENTANEDIAL × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
6T93 Nucleosome with OCT4-SOX2 motif at SHL-6 Deposited 2019-10-25 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.49 Å
6V92 RSC-NCP Deposited 2019-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 33 PDB declaration: 35-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 20.00 Å
6YOV OCT4-SOX2-bound nucleosome - SHL+6 Deposited 2020-04-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded PTD PENTANEDIAL × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.42 Å
7BWD Structure of Dot1L-H2BK34ub Nucleosome Complex Deposited 2020-04-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.32 Å
7BXT The cryo-EM structure of CENP-A nucleosome in complex with CENP-C peptide and CENP-N N-terminal domain Deposited 2020-04-20 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7BY0 The cryo-EM structure of CENP-A nucleosome in complex with the phosphorylated CENP-C Deposited 2020-04-21 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7C0M Human cGAS-nucleosome complex Deposited 2020-05-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Chain c 2–130（129 aa）
Chain g 2–130（129 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7CCQ Structure of the 1:1 cGAS-nucleosome complex Deposited 2020-06-17 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 16–118（103 aa）
Chain G 16–118（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7CCR Structure of the 2:2 cGAS-nucleosome complex Deposited 2020-06-17 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain C 16–118（103 aa）
Chain G 16–118（103 aa）
Chain N 16–118（103 aa）
Chain R 16–118（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.90 Å
7COW 353 bp di-nucleosome harboring cohesive DNA termini with linker histone H1.0 Deposited 2020-08-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CA CALCIUM ION × 3 K POTASSIUM ION × 5 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；potassium acetate, calcium chloride, potassium chloride
Resolution 2.86 Å R-free 0.297
7D1Z Cryo-EM structure of SET8-nucleosome complex Deposited 2020-09-15 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
7D20 Cryo-EM structure of SET8-CENP-A-nucleosome complex Deposited 2020-09-15 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7DBP Linker histone defines structure and self-association behaviour of the 177 bp human chromosome Deposited 2020-10-21 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7K5X Cryo-EM structure of a chromatosome containing human linker histone H1.0 Deposited 2020-09-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.93 Å
7K5Y Cryo-EM structure of a chromatosome containing human linker histone H1.4 Deposited 2020-09-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
7K60 Cryo-EM structure of a chromatosome containing human linker histone H1.10 Deposited 2020-09-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
7K61 Cryo-EM structure of 197bp nucleosome aided by scFv Deposited 2020-09-17 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.85 Å
7K63 Cryo-EM structure of a chromatosome containing chimeric linker histone gH1.10-ncH1.4 Deposited 2020-09-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
7LYA Cryo-EM structure of the human nucleosome core particle with linked histone proteins H2A and H2B Deposited 2021-03-06 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 13–130（118 aa）
Chain G 13–130（118 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.91 Å
7LYB Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c Deposited 2021-03-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 13–130（118 aa）
Chain G 13–130（118 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.28 Å
7LYC Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A Lys13 and Lys15 in complex with BARD1 (residues 415-777) Deposited 2021-03-06 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 13–130（118 aa）
Chain G 13–130（118 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
7NL0 Cryo-EM structure of the Lin28B nucleosome core particle Deposited 2021-02-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7PET The 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 34 PDB declaration: 36-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Chain m 1–130（130 aa）
Chain q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.50 Å
7PEU Trinucleosome of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
7PEV Nucleosome stack of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.00 Å
7PEW Nucleosome 1 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
7PEX Nucleosome 2 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
7PEY Nucleosome 3 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7PEZ Nucleosome 4 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain m 1–130（130 aa）
Chain q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.90 Å
7PF0 Trinucleosome of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.00 Å
7PF2 Nucleosome stack of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
7PF3 Nucleosome 4 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain m 1–130（130 aa）
Chain q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7PF4 Nucleosome 3 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7PF5 Nucleosome 2 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7PF6 Nucleosome 1 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7PFA Trinucleosome of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.70 Å
7PFC Nucleosome stack of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
7PFD Nucleosome 1 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7PFE Nucleosome 2 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7PFF Nucleosome 3 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7PFT Trinucleosome of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.80 Å
7PFU Nucleosome stack of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.00 Å
7PFV Nucleosome 1 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7PFW Nucleosome 2 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.20 Å
7PFX Nucleosome 3 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7V90 Telomeric mononucleosome Deposited 2021-08-24 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7V96 Telomeric Dinucleosome Deposited 2021-08-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.92 Å
7V99 catalytic core of human telomerase holoenzyme Deposited 2021-08-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: pentameric
Chain K 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7V9C Telomeric Dinucleosome in open state Deposited 2021-08-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7V9J Telomeric trinucleosome Deposited 2021-08-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain U 1–130（130 aa）
Chain Y 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.00 Å
7V9K Telomeric tetranucleosome Deposited 2021-08-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 34-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain U 1–130（130 aa）
Chain Y 1–130（130 aa）
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.10 Å
7V9S Telomeric trinucleosome in open state Deposited 2021-08-26 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain U 1–130（130 aa）
Chain Y 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.00 Å
7VA4 Telomeric tetranucleosome in open state Deposited 2021-08-27 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 34-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain U 1–130（130 aa）
Chain Y 1–130（130 aa）
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 14.00 Å
7VZ4 Cryo-EM structure of human nucleosome core particle composed of the Widom 601L DNA sequence Deposited 2021-11-15 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 1.89 Å
7W9V Cryo-EM structure of nucleosome in complex with p300 acetyltransferase catalytic core (complex I) Deposited 2021-12-10 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.95 Å
7WBV RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome Deposited 2021-12-17 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain c 2–130（129 aa）
Chain g 2–130（129 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7WBW RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3.5) of the nucleosome Deposited 2021-12-17 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain c 2–130（129 aa）
Chain g 2–130（129 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.10 Å
7WBX RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome Deposited 2021-12-17 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain c 2–130（129 aa）
Chain g 2–130（129 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7XD1 cryo-EM structure of unmodified nucleosome Deposited 2022-03-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 11–119（109 aa）
Chain G 11–119（109 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7XSE RNA polymerase II elongation complex transcribing a nucleosome (EC42) Deposited 2022-05-13 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7XSX RNA polymerase II elongation complex transcribing a nucleosome (EC49) Deposited 2022-05-15 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7XSZ RNA polymerase II elongation complex transcribing a nucleosome (EC115) Deposited 2022-05-15 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7XT7 RNA polymerase II elongation complex transcribing a nucleosome (EC49B) Deposited 2022-05-16 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7XTD RNA polymerase II elongation complex transcribing a nucleosome (EC58oct) Deposited 2022-05-16 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7XTI RNA polymerase II elongation complex transcribing a nucleosome (EC58hex) Deposited 2022-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7XVL Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an DNA fragment) Deposited 2022-05-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain W 1–130（130 aa）
Chain a 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 3.51 Å R-free 0.280
7XVL Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an DNA fragment) Deposited 2022-05-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain g 1–130（130 aa）
Chain k 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 3.51 Å R-free 0.280
7XVM Crystal Structure of Nucleosome-H5 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CA CALCIUM ION × 18 CL CHLORIDE ION × 3 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 2.84 Å R-free 0.259
7XX5 Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CA CALCIUM ION × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 3.19 Å R-free 0.259
7XX6 Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CA CALCIUM ION × 21 K POTASSIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 3.39 Å R-free 0.296
7XX6 Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric
Chain W 1–130（130 aa）
Chain a 1–130（130 aa）
Chain g 1–130（130 aa）
Chain k 1–130（130 aa）
Not recorded CA CALCIUM ION × 26 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 3.39 Å R-free 0.296
7XZX Cryo-EM structure of the nucleosome in complex with p53 DNA-binding domain Deposited 2022-06-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.53 Å
7XZY Cryo-EM structure of the nucleosome containing 193 base-pair DNA with a p53 target sequence Deposited 2022-06-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.97 Å
7XZZ Cryo-EM structure of the nucleosome in complex with p53 Deposited 2022-06-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.07 Å
7Y00 Cryo-EM structure of the nucleosome containing 169 base-pair DNA with a p53 target sequence Deposited 2022-06-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.96 Å
7Y7I chicken KNL2 in complex with the CENP-A nucleosome Deposited 2022-06-22 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Mutation：L51M, L58M, L93M Mutation：L51M, L58M, L93M No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.42 Å
7ZI4 Cryo-EM structure of the human INO80 complex bound to a WT nucleosome Deposited 2022-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain K 1–130（130 aa）
Chain O 1–130（130 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；4uL of sample applied to Quantifoil R2/2 Cu 300 mesh grids. blot parameters were wait time 30 sec, blot time 0.5 sec, blot force -8
Resolution 3.20 Å
8G57 Structure of nucleosome-bound Sirtuin 6 deacetylase Deposited 2023-02-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；12.5 mM HEPES pH 7.5, 60 mM KCl, 1.5% glycerol, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
8GRM Cryo-EM structure of PRC1 bound to H2AK119-UbcH5b-Ub nucleosome Deposited 2022-09-02 Different construct Different oligomeric state Different ligand/ion Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 12–120（109 aa）
Chain G 12–120（109 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
8H0V RNA polymerase II transcribing a chromatosome (type I) Deposited 2022-09-30 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8H0W RNA polymerase II transcribing a chromatosome (type II) Deposited 2022-09-30 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8HAG Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 1 (3.2 angstrom resolution) Deposited 2022-10-26 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8HAH Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 2 (3.9 angstrom resolution) Deposited 2022-10-26 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8HAI Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 1 (4.7 angstrom resolution) Deposited 2022-10-26 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
8HAJ Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 2 (4.8 angstrom resolution) Deposited 2022-10-26 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
8HAK Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 4 (4.5 angstrom resolution) Deposited 2022-10-26 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
8HAL Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 1 Deposited 2022-10-26 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8HAM Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 2 Deposited 2022-10-26 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
8HAN Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 3 Deposited 2022-10-26 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
8HE5 RNA polymerase II elongation complex bound with Rad26 and Elf1, stalled at SHL(-3.5) of the nucleosome Deposited 2022-11-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 25-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.95 Å
8HR1 Cryo-EM structure of SSX1 bound to the unmodified nucleosome at a resolution of 3.02 angstrom Deposited 2022-12-14 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 14–119（106 aa）
Chain G 14–119（106 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.02 Å
8I17 Structural basis for H2A-H2B recognitions by human Spt16 Deposited 2023-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 14–113（100 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M MES monohydrate pH 6.0, 14% w/v Polyethylene glycol 4,000
Resolution 1.98 Å R-free 0.211
8I17 Structural basis for H2A-H2B recognitions by human Spt16 Deposited 2023-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 14–113（100 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M MES monohydrate pH 6.0, 14% w/v Polyethylene glycol 4,000
Resolution 1.98 Å R-free 0.211
8I17 Structural basis for H2A-H2B recognitions by human Spt16 Deposited 2023-01-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 14–113（100 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M MES monohydrate pH 6.0, 14% w/v Polyethylene glycol 4,000
Resolution 1.98 Å R-free 0.211
8IEG Bre1(mRBD-RING)/Rad6-Ub/nucleosome complex Deposited 2023-02-15 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 11–119（109 aa）
Chain G 11–119（109 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.44 Å
8IEJ RNF20-RNF40/hRad6A-Ub/nucleosome complex Deposited 2023-02-15 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 11–119（109 aa）
Chain G 11–119（109 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
8IHL Overlapping tri-nucleosome Deposited 2023-02-23 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain O 1–130（130 aa）
Chain S 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.64 Å
8JBX Human canonical 601 DNA nucleosome Deposited 2023-05-09 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
8JCC Human histone H2B variant H2BFWT Cryo-EM structure with 601 DNA sequence Deposited 2023-05-10 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.42 Å
8JCD Human H2BFWTH100R nucleosome with 601 DNA Deposited 2023-05-11 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.14 Å
8JH2 RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.70 Å
8JH3 RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8JH4 RNA polymerase II elongation complex containing 60 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8JHG Native SUV420H1 bound to 167-bp nucleosome Deposited 2023-05-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 16–130（115 aa）
Chain G 16–130（115 aa）
Not recorded ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane
Resolution 3.58 Å
8JL9 Cryo-EM structure of the human nucleosome with scFv Deposited 2023-06-02 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.65 Å
8JLA Cryo-EM structure of the human nucleosome lacking N-terminal region of H2A, H2B, H3, and H4 Deposited 2023-06-02 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 11–130（120 aa）
Chain G 11–130（120 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.44 Å
8JLB Cryo-EM structure of the 145 bp human nucleosome containing H3.2 C110A mutant Deposited 2023-06-02 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.36 Å
8JLD Cryo-EM structure of the 145 bp human nucleosome containing acetylated H3 tail Deposited 2023-06-02 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.48 Å
8JND The cryo-EM structure of the nonameric RAD51 ring bound to the nucleosome with the linker DNA binding Deposited 2023-06-06 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 19-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.66 Å
8JNE The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome without the linker DNA binding Deposited 2023-06-06 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.68 Å
8JNF The cryo-EM structure of the RAD51 filament bound to the nucleosome Deposited 2023-06-06 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.91 Å
8KB5 Cryo-EM structure of the human nucleosome containing H3.8 Deposited 2023-08-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.26 Å
8KCY Structure of nucleosome complexed with two DEK molecules Deposited 2023-08-08 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8KD1 Structure of nucleosome complexed with one DEK molecule Deposited 2023-08-08 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8KE0 Structure of H1.2 bound to the nucleosome Deposited 2023-08-11 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8OSJ Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL-6.2 (DNA conformation 1) Deposited 2023-04-19 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
8OSK Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL+5.8 (composite map) Deposited 2023-04-19 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8OSL Cryo-EM structure of CLOCK-BMAL1 bound to the native Por enhancer nucleosome (map 2, additional 3D classification and flexible refinement) Deposited 2023-04-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.90 Å
8OTS OCT4 and MYC-MAX co-bound to a nucleosome Deposited 2023-04-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded PTD PENTANEDIAL × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8OTT MYC-MAX bound to a nucleosome at SHL+5.8 Deposited 2023-04-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 9–117（109 aa）
Not recorded PTD PENTANEDIAL × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8Q36 Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Foamy Virus GAG Peptide-Au[I] Compound) Deposited 2023-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain CCC 14–120（107 aa）
Chain GGG 14–120（107 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0].
Resolution 2.60 Å R-free 0.262
8Q3E High Resolution Structure of Nucleosome Core with Bound Foamy Virus GAG Peptide Deposited 2023-08-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain CCC 14–120（107 aa）
Chain GGG 14–120（107 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
Resolution 2.17 Å R-free 0.270
8Q3M Structure of Nucleosome Core with a Bound Kaposi Sarcoma Associated Herpesvirus LANA Peptide Having a Methionine to Ornithine Substitution Deposited 2023-08-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain CCC 14–120（107 aa）
Chain GGG 14–120（107 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
Resolution 2.50 Å R-free 0.268
8Q3X Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Kaposi Sarcoma Associated Herpesvirus LANA Peptide-Au[I] Compound) Deposited 2023-08-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain CCC 14–120（107 aa）
Chain GGG 14–120（107 aa）
Not recorded AU GOLD ION × 1 XIS 4-diphenylphosphanylbenzoic acid × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
Resolution 2.30 Å R-free 0.262
8RGM Cryo-EM structure of nucleosome containing Widom603 DNA Deposited 2023-12-14 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8SMW Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 1) Deposited 2023-04-26 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8SMX Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 2) Deposited 2023-04-26 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SMY Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 3) Deposited 2023-04-26 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SMZ Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (Class 4) Deposited 2023-04-26 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SN0 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 5) Deposited 2023-04-26 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SN1 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 6) Deposited 2023-04-26 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8SN2 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c (UbcH5c chemically conjugated to histone H2A) Deposited 2023-04-26 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8SN3 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8SN4 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN5 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 3) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8SN6 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 4) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN7 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 5) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN8 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 6) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN9 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8SNA Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8TXV Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 1) Deposited 2023-08-24 Different construct Different mutation/modification Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：K13S Mutation：K13S No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8TXW Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 2) Deposited 2023-08-24 Different construct Different mutation/modification Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：K13S Mutation：K13S No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8TXX Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 3) Deposited 2023-08-24 Different construct Different mutation/modification Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：K13S Mutation：K13S No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8U13 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 1) Deposited 2023-08-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 13–130（118 aa）
Chain G 13–130（118 aa）
Mutation：K13S Mutation：K13S ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8U14 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 2) Deposited 2023-08-30 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 13–130（118 aa）
Chain G 13–130（118 aa）
Mutation：K13S Mutation：K13S ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8U9S Cryo-EM structure of NRCAM nucleosome aided by scFv Deposited 2023-09-20 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8UBJ Cryo-EM structure of NRCAM nucleosome aided by scFv (3D Flex map) Deposited 2023-09-23 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8UBK Cryo-EM structure of Ascl1/E12a in complex with NRCAM nucleosome Deposited 2023-09-23 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8UBL Cryo-EM structure of Ascl1/E12a in complex with NRCAM nucleosome (3D Flex map) Deposited 2023-09-23 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8UPF Cryo-EM structure of the human nucleosome core particle in complex with RNF168-UbcH5c Deposited 2023-10-22 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 13–130（118 aa）
Chain G 13–130（118 aa）
Mutation：R11S Mutation：R11S ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8UQ8 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 2-residue linker Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 13–106（94 aa）
Not recorded CL CHLORIDE ION × 7 GOL GLYCEROL × 3 ZN ZINC ION × 2 NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (9.5 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.34 Å R-free 0.236
8UQ8 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 2-residue linker Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain a 13–106（94 aa）
Not recorded CL CHLORIDE ION × 14 GOL GLYCEROL × 2 ZN ZINC ION × 2 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (9.5 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.34 Å R-free 0.236
8UQ9 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 4-residue linker Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 13–106（94 aa）
Not recorded CL CHLORIDE ION × 17 GOL GLYCEROL × 3 ZN ZINC ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (8.8 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.30 Å R-free 0.206
8UQ9 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 4-residue linker Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain a 13–106（94 aa）
Not recorded CL CHLORIDE ION × 19 GOL GLYCEROL × 3 ZN ZINC ION × 2 NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (8.8 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.30 Å R-free 0.206
8UQA Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 12-residue linker Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain K 13–106（94 aa）
Mutation：C85K in UbcH5c NA SODIUM ION × 3 ZN ZINC ION × 2 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (8.0 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.05 Å R-free 0.231
8UQB Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (crystallization condition 1) Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 13–106（94 aa）
Mutation：C85K in UbcH5c ZN ZINC ION × 2 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (12 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 50 mM BIS-TRIS propane, pH 7.0, 1 M NaCl
Resolution 2.48 Å R-free 0.260
8UQC Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (crystallization condition 2) Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 13–106（94 aa）
Mutation：C85K in UbcH5c ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (12 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 4% tacsimate, pH 6, 13.5% PEG3350
Resolution 2.61 Å R-free 0.252
8UQD Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (condition 2. RING not modeled in density) Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 13–106（94 aa）
Mutation：C85K in UbcH5c No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (12 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 4% tacsimate, pH 6, 13.5% PEG3350
Resolution 3.89 Å R-free 0.322
8UQE Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 26-residue linker (RING not modeled in density) Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 13–106（94 aa）
Mutation：S22R,C85K in UbcH5c No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (10 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M imidazole, pH 6.5, 1.0 M sodium acetate
Resolution 3.56 Å R-free 0.268
8VFX Cryo-EM structure of 186bp ALBN1 nucleosome aided by scFv Deposited 2023-12-22 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.65 Å
8VFY Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 1) Deposited 2023-12-22 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.89 Å
8VFZ Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 2) Deposited 2023-12-22 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8VG0 Cryo-EM structure of GATA4 in complex with ALBN1 nucleosome Deposited 2023-12-22 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
8VG1 Cryo-EM structure of FoxA1 and GATA4 in complex with ALBN1 nucleosome Deposited 2023-12-22 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.48 Å
8VG2 Cryo-EM structure of FoxA1 and GATA4 in complex with H14 chromatosome Deposited 2023-12-22 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
8VLR Cryo-EM structure of native H2AK119bu nucleosome at 2.6 Deposited 2024-01-12 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 12–119（108 aa）
Chain G 12–119（108 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Tris-HCl, pH 7.5, 50 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8W9D Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 1 Deposited 2023-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 7 K POTASSIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8W9E Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 2 Deposited 2023-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 7 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8W9F Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 3 Deposited 2023-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8WG5 Cryo-EM structure of USP16 bound to H2AK119Ub nucleosome Deposited 2023-09-20 Different construct Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 11–119（109 aa）
Chain G 11–119（109 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
8X7I Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by intein-based E2-Ub-NCP conjugation strategy Deposited 2023-11-24 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 11–121（111 aa）
Chain G 11–119（109 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
8X7J Cryo-EM structures of RNF168/UbcH5c-Ub/nucleosomes complex determined by activity-based chemical trapping strategy Deposited 2023-11-24 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 12–119（108 aa）
Chain G 11–118（108 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
8X7K Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination) Deposited 2023-11-24 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 15–119（105 aa）
Chain G 11–118（108 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
8XBT The cryo-EM structure of the octameric RAD51 ring bound to the nucleosome with the linker DNA binding Deposited 2023-12-07 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.12 Å
8XBU The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome with the linker DNA binding Deposited 2023-12-07 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.24 Å
8XRJ RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei Deposited 2024-01-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain c 2–130（129 aa）
Chain g 2–130（129 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8XVS RNA polymerase II elongation complex with downstream nucleosome extracted from human nuclei Deposited 2024-01-15 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain c 2–130（129 aa）
Chain g 2–130（129 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8Y3C Cryo-EM structure of the overlapping di-nucleosome (closed form) Deposited 2024-01-29 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.21 Å
8Y3D Cryo-EM structure of the overlapping di-nucleosome (intermediate form2) Deposited 2024-01-29 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
8Y3E Cryo-EM structure of the overlapping di-nucleosome (open form) Deposited 2024-01-29 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.32 Å
8Y3F Cryo-EM structure of the overlapping di-nucleosome (intermediate form1) Deposited 2024-01-29 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.54 Å
8YBJ Cryo-EM structure of human nucleosome core particle composed of the Widom 601 DNA sequence Deposited 2024-02-14 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.38 Å
8YBK Cryo-EM structure of the human nucleosome containing the H3.1 E97K mutant Deposited 2024-02-14 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.69 Å
8YNY Structure of Cas9-sgRNA ribonucleoprotein bound to nucleosome Deposited 2024-03-12 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: 13-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.52 Å
8YTI Crystal Structure of Nucleosome-H1x Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2024-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CL CHLORIDE ION × 8 CA CALCIUM ION × 52 K POTASSIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45 mM CaCl2, 25 mM KCl, 10 mM Na-acetate (pH 4.5)
Resolution 2.70 Å R-free 0.267
8YV8 Cryo-EM structure of CDCA7 bound to nucleosome including hemimethylated CpG site in Widom601 positioning sequence. Deposited 2024-03-28 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8ZJR Structure of nucleosome-bound RFX5 complex Deposited 2024-05-15 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8ZJT Structure of free nucleosome Deposited 2024-05-15 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9BE5 Cryo-EM structure of Human Nucleosome collected by EPU on Glacios at 3.3 Angstrom resolution Deposited 2024-04-14 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain G 15–119（105 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9BE6 Cryo-EM structure of Human Nucleosome collected by Leginon on Krios at 3.0 Angstrom resolution Deposited 2024-04-14 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain G 15–119（105 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9GE5 CryoEM structure of the human INO80-Hexasome complex Deposited 2024-08-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain S 12–119（108 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
9GEL CryoEM structure of the human INO80-Hexasome complex Deposited 2024-08-07 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain S 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.86 Å
9GEV CryoEM structure of the human INO80 core-nucleosome complex state N-6 Deposited 2024-08-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain O 2–130（129 aa）
Chain S 2–130（129 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
9GF6 CryoEM structure of the human INO80 core-nucleosome complex state N-6 Deposited 2024-08-08 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain O 2–130（129 aa）
Chain S 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9GFB CryoEM structure of the human INO80 core-nucleosome complex state N-7 Deposited 2024-08-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain O 2–130（129 aa）
Chain S 2–130（129 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 6 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
9GFM CryoEM structure of the human INO80 core-nucleosome complex state N-7 Deposited 2024-08-09 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain O 14–119（106 aa）
Chain S 9–119（111 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9GW2 State 2 MAP 1 SETD2 bound to proximal H3 of upstream nucleosome Deposited 2024-09-26 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.84 Å
9IGW Ku70/80 bound to 147 bp nucleosome Deposited 2025-02-20 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å
9IGX Ku70/80 bound to 153 bp nucleosome Deposited 2025-02-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain C 12–121（110 aa）
Chain G 12–121（110 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.56 Å
9IPU cryo-EM structure of the RNF168(1-193)/UbcH5c-Ub ubiquitylation module bound to H1.0-K63-Ub3 modified chromatosome Deposited 2024-07-11 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
9J0N Paused elongation complex of mammalian RNA polymerase II with nucleosome (PEC2-nuc) Deposited 2024-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 27 PDB declaration: 30-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9J0O Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC1-nuc) Deposited 2024-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9J0P Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC2-nuc) Deposited 2024-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9J8M Cryo-EM structure of BAF-Lamin A/C IgF-nucleosome complex (High mobility complex) Deposited 2024-08-21 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.82 Å
9J8N Cryo-EM structure of BAF-Lamin A/C IgF-nucleosome complex (Low mobility complex) Deposited 2024-08-21 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 32-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.14 Å
9J8O Cryo-EM structure of BAF-Lamin A/C IgF-H1-nucleosome complex Deposited 2024-08-21 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 28-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.05 Å
9J8W Cryo-EM structure of NCP-UV-DDB complex containing CPD Deposited 2024-08-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.38 Å
9JC6 Human H2BW2 nucleosome Deposited 2024-08-28 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.34 Å
9KQO cryo-EM structure of RNF20/RNF40-RAD6A-Ub in complex with H2BS112GlcNAc nucleosome Deposited 2024-11-26 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded ZN ZINC ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.48 Å
9L1X hDEK-nucleosome complex (conformation 1) Deposited 2024-12-16 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 2–120（119 aa）
Chain G 2–120（119 aa）
Not recorded UNX UNKNOWN LIGAND × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.69 Å
9L22 hDEK-nucleosome complex (conformation 2) Deposited 2024-12-16 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded UNX UNKNOWN LIGAND × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9R04 p53 bound to the nucleosome at position SHL-5.7 (crosslinked sample) Deposited 2025-04-24 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9R2M p53 bound to nucleosome at position SHL+5.9 (non-crosslinked sample, composite map) Deposited 2025-04-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9R2P p53 bound to nucleosome at position SHL+5.9 (crosslinked sample) Deposited 2025-04-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.18 Å
9R2Q p53 bound to nucleosome at position SHL-5.7 (non-crosslinked sample) Deposited 2025-04-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9RL4 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL-6 Deposited 2025-06-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded PTD PENTANEDIAL × 16 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9RMC Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 1 Deposited 2025-06-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9RN1 Structure of BAF-nucleosome complex with OCT4-SOX2 at SHL+6 in ADP-bound state, BAF47 bound to ATPase lobe 2 Deposited 2025-06-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.90 Å
9RN2 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 2 Deposited 2025-06-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 19 PDB declaration: 21-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
9RZC State 3 MAP 1 SETD2 bound to distal H3 of upstream nucleosome Deposited 2025-07-15 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.66 Å
9RZE State 2 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to proximal upstream H3 Deposited 2025-07-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.53 Å
9S0U State 3 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to distal upstream H3 Deposited 2025-07-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.72 Å
9S3G State 1 MAP3 RNA Pol II activated elongation complex with SETD2 and upstream hexasome Deposited 2025-07-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
9U5U The 1:1 cryo-EM structure of BAP1/ASXL1-K351Ub in complex with H2AK119Ub nucleosome Deposited 2025-03-21 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
9UZ7 Cryo-EM structure of the nucleosome core particle with site-specific DNA-histone crosslinking Deposited 2025-05-16 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain E 2–130（129 aa）
Chain F 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；10 mM HEPES, pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution not provided
9WMS Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type B) Deposited 2025-09-03 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9WMT Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type A) Deposited 2025-09-03 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
9WMU Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type A) Deposited 2025-09-03 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.28 Å
9WMV Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type B) Deposited 2025-09-03 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.66 Å
9WMW Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, FACT-hexamer) Deposited 2025-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
9XSF Cryo-EM structure of H4S47GlcNAc nucleosome at 3.39 angstrom Deposited 2025-11-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.39 Å
9YL3 State 1 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.50 Å
9YLE State 3 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.63 Å
9YLY MLL4FC bound to a nucleosome with p53 RE Deposited 2025-10-09 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 14 PDB declaration: 16-meric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.77 Å
9YM8 State 2 focused on PHD FYR of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.43 Å
9YMF State 2 focused on H3 N terminal tail of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.45 Å
9ZEN Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1B2 Deposited 2025-11-30 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain C 11–121（111 aa）
Chain G 11–121（111 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES pH7.6, 50 mM NaCl, 0.5 mM MgCl2, 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.17 Å
9ZEO Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1G1 Deposited 2025-11-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 11–121（111 aa）
Chain G 11–121（111 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES pH7.6, 50 mM NaCl, 0.5 mM MgCl2, 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å

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

View Construct and Data Evidence
UniProt name H2A1B_HUMAN
Isoform —
PDB entities 3, 6
Chains and sequence ranges Author chain C； PDBConstruct 1–106； UniProt 14–119 Author chain G； PDBConstruct 1–106； UniProt 14–119

Histone H2B type 1-K

Homo sapiens

UniProt O60814

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 10 DNA 2 PDB declaration: dodecameric（12） Consistent with all polymer counts Chain D； UniProt 35–125 Chain H； UniProt 35–125 Not recorded Histone H3 × 2 （A0A653DHJ5） Histone H4 (Fragment) × 1 （A0A093PN76） Histone H2A type 1-B/E × 1 （P04908） Histone H4 × 1 （A0A8C2GGI7） Histone H2A type 1-B/E × 1 （P04908） Protein SSX2 × 1 （Q16385） Polyubiquitin-B (Fragment) × 1 （J3QS39） DNA (137-MER) × 1 DNA (136-MER) × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.05 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 8HQY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2CV5 Crystal structure of human nucleosome core particle Deposited 2005-05-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 0–125（126 aa）
Chain H 0–125（126 aa）
Not recorded MN MANGANESE (II) ION × 9 CL CHLORIDE ION × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.277
6KE9 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-07-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 32–126（95 aa）
Chain H 32–126（95 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
Resolution 2.22 Å R-free 0.230
6L9H The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-11-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 32–126（95 aa）
Chain H 32–126（95 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
Resolution 2.60 Å R-free 0.278
6LE9 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-11-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 32–126（95 aa）
Chain H 32–126（95 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
Resolution 2.60 Å R-free 0.281
6T79 Structure of a human nucleosome at 3.2 A resolution Deposited 2019-10-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 3.20 Å
6T7A Structure of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 3.70 Å
6T7B Structure of human Sox2 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 5.10 Å
6T7C Structure of two copies of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 4.00 Å
6T7D Structure of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 4.40 Å
6V92 RSC-NCP Deposited 2019-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 33 PDB declaration: 35-meric
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 20.00 Å
6Y5D Structure of human cGAS (K394E) bound to the nucleosome Deposited 2020-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain P 1–126（126 aa）
Chain T 1–126（126 aa）
Not recorded PTD PENTANEDIAL × 9 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6Y5E Structure of human cGAS (K394E) bound to the nucleosome (focused refinement of cGAS-NCP subcomplex) Deposited 2020-02-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 33–125（93 aa）
Chain H 32–125（94 aa）
Not recorded PTD PENTANEDIAL × 8 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
7BWD Structure of Dot1L-H2BK34ub Nucleosome Complex Deposited 2020-04-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.32 Å
7DBP Linker histone defines structure and self-association behaviour of the 177 bp human chromosome Deposited 2020-10-21 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7JZV Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome Deposited 2020-09-02 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain O 2–126（125 aa）
Chain o 2–126（125 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7PET The 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 34 PDB declaration: 36-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Chain n 1–126（126 aa）
Chain r 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.50 Å
7PEU Trinucleosome of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
7PEV Nucleosome stack of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.00 Å
7PEW Nucleosome 1 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
7PEX Nucleosome 2 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
7PEY Nucleosome 3 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7PEZ Nucleosome 4 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain e 1–126（126 aa）
Chain n 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.90 Å
7PF0 Trinucleosome of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.00 Å
7PF2 Nucleosome stack of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
7PF3 Nucleosome 4 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain n 1–126（126 aa）
Chain r 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7PF4 Nucleosome 3 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7PF5 Nucleosome 2 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7PF6 Nucleosome 1 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7PFA Trinucleosome of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.70 Å
7PFC Nucleosome stack of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
7PFD Nucleosome 1 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7PFE Nucleosome 2 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7PFF Nucleosome 3 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7PFT Trinucleosome of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.80 Å
7PFU Nucleosome stack of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.00 Å
7PFV Nucleosome 1 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7PFW Nucleosome 2 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.20 Å
7PFX Nucleosome 3 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7V90 Telomeric mononucleosome Deposited 2021-08-24 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 28–126（99 aa）
Chain H 28–126（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7V96 Telomeric Dinucleosome Deposited 2021-08-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain D 28–126（99 aa）
Chain H 28–126（99 aa）
Chain N 28–126（99 aa）
Chain R 28–126（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.92 Å
7V99 catalytic core of human telomerase holoenzyme Deposited 2021-08-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: pentameric
Chain L 2–126（125 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7V9C Telomeric Dinucleosome in open state Deposited 2021-08-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain D 32–126（95 aa）
Chain H 32–126（95 aa）
Chain N 32–126（95 aa）
Chain R 32–126（95 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7V9J Telomeric trinucleosome Deposited 2021-08-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain D 28–126（99 aa）
Chain H 28–126（99 aa）
Chain N 28–126（99 aa）
Chain R 28–126（99 aa）
Chain V 28–126（99 aa）
Chain Z 28–126（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.00 Å
7V9K Telomeric tetranucleosome Deposited 2021-08-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 34-meric
Chain D 28–126（99 aa）
Chain H 28–126（99 aa）
Chain N 28–126（99 aa）
Chain R 28–126（99 aa）
Chain V 28–126（99 aa）
Chain Z 28–126（99 aa）
Chain d 28–126（99 aa）
Chain h 28–126（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.10 Å
7V9S Telomeric trinucleosome in open state Deposited 2021-08-26 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain D 28–126（99 aa）
Chain H 28–126（99 aa）
Chain N 28–126（99 aa）
Chain R 28–126（99 aa）
Chain V 28–126（99 aa）
Chain Z 28–126（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.00 Å
7VA4 Telomeric tetranucleosome in open state Deposited 2021-08-27 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 34-meric
Chain D 32–126（95 aa）
Chain H 32–126（95 aa）
Chain N 32–126（95 aa）
Chain R 32–126（95 aa）
Chain V 32–126（95 aa）
Chain Z 32–126（95 aa）
Chain d 32–126（95 aa）
Chain h 32–126（95 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 14.00 Å
7XCR Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 1:1 complex Deposited 2022-03-25 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 32–125（94 aa）
Chain H 32–125（94 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.57 Å
7XCT Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 2:1 complex Deposited 2022-03-25 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 33–125（93 aa）
Chain H 33–125（93 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
7XD1 cryo-EM structure of unmodified nucleosome Deposited 2022-03-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 32–125（94 aa）
Chain H 32–125（94 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8GRM Cryo-EM structure of PRC1 bound to H2AK119-UbcH5b-Ub nucleosome Deposited 2022-09-02 Different construct Different oligomeric state Different ligand/ion Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 31–126（96 aa）
Chain H 32–126（95 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
8HR1 Cryo-EM structure of SSX1 bound to the unmodified nucleosome at a resolution of 3.02 angstrom Deposited 2022-12-14 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain D 35–125（91 aa）
Chain H 35–125（91 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.02 Å
8IEG Bre1(mRBD-RING)/Rad6-Ub/nucleosome complex Deposited 2023-02-15 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain D 32–125（94 aa）
Chain H 32–125（94 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.44 Å
8IEJ RNF20-RNF40/hRad6A-Ub/nucleosome complex Deposited 2023-02-15 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain D 32–125（94 aa）
Chain H 32–125（94 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
8JHF Native SUV420H1 bound to 167-bp nucleosome Deposited 2023-05-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 32–126（95 aa）
Chain H 32–126（95 aa）
Not recorded ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane
Resolution 3.68 Å
8JHG Native SUV420H1 bound to 167-bp nucleosome Deposited 2023-05-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 32–126（95 aa）
Chain H 32–126（95 aa）
Not recorded ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane
Resolution 3.58 Å
8Q36 Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Foamy Virus GAG Peptide-Au[I] Compound) Deposited 2023-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain DDD 32–126（95 aa）
Chain HHH 32–126（95 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0].
Resolution 2.60 Å R-free 0.262
8Q3E High Resolution Structure of Nucleosome Core with Bound Foamy Virus GAG Peptide Deposited 2023-08-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain DDD 32–126（95 aa）
Chain HHH 32–126（95 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
Resolution 2.17 Å R-free 0.270
8Q3M Structure of Nucleosome Core with a Bound Kaposi Sarcoma Associated Herpesvirus LANA Peptide Having a Methionine to Ornithine Substitution Deposited 2023-08-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain DDD 32–126（95 aa）
Chain HHH 32–126（95 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
Resolution 2.50 Å R-free 0.268
8Q3X Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Kaposi Sarcoma Associated Herpesvirus LANA Peptide-Au[I] Compound) Deposited 2023-08-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain DDD 32–126（95 aa）
Chain HHH 32–126（95 aa）
Not recorded AU GOLD ION × 1 XIS 4-diphenylphosphanylbenzoic acid × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
Resolution 2.30 Å R-free 0.262
8W9D Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 1 Deposited 2023-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded ZN ZINC ION × 7 K POTASSIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8W9E Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 2 Deposited 2023-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded ZN ZINC ION × 7 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8W9F Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 3 Deposited 2023-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8WG5 Cryo-EM structure of USP16 bound to H2AK119Ub nucleosome Deposited 2023-09-20 Different construct Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 32–125（94 aa）
Chain H 32–125（94 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
8X7I Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by intein-based E2-Ub-NCP conjugation strategy Deposited 2023-11-24 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain D 32–125（94 aa）
Chain H 32–125（94 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
8X7J Cryo-EM structures of RNF168/UbcH5c-Ub/nucleosomes complex determined by activity-based chemical trapping strategy Deposited 2023-11-24 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain D 32–125（94 aa）
Chain H 32–125（94 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
8X7K Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination) Deposited 2023-11-24 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 32–125（94 aa）
Chain H 32–125（94 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
8YV8 Cryo-EM structure of CDCA7 bound to nucleosome including hemimethylated CpG site in Widom601 positioning sequence. Deposited 2024-03-28 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8ZJR Structure of nucleosome-bound RFX5 complex Deposited 2024-05-15 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8ZJT Structure of free nucleosome Deposited 2024-05-15 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9D3R 147-bp 5S rDNA nucleosome - closed Deposited 2024-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 30–125（96 aa）
Chain H 30–125（96 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9ECP Structure of the native human NCP purified from HEK293 cells Deposited 2024-11-14 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 32–125（94 aa）
Chain H 32–125（94 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.91 Å
9GW2 State 2 MAP 1 SETD2 bound to proximal H3 of upstream nucleosome Deposited 2024-09-26 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.84 Å
9IPU cryo-EM structure of the RNF168(1-193)/UbcH5c-Ub ubiquitylation module bound to H1.0-K63-Ub3 modified chromatosome Deposited 2024-07-11 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
9KQO cryo-EM structure of RNF20/RNF40-RAD6A-Ub in complex with H2BS112GlcNAc nucleosome Deposited 2024-11-26 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded ZN ZINC ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.48 Å
9RZC State 3 MAP 1 SETD2 bound to distal H3 of upstream nucleosome Deposited 2025-07-15 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.66 Å
9RZE State 2 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to proximal upstream H3 Deposited 2025-07-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.53 Å
9S0U State 3 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to distal upstream H3 Deposited 2025-07-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.72 Å
9S3G State 1 MAP3 RNA Pol II activated elongation complex with SETD2 and upstream hexasome Deposited 2025-07-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain h 1–126（126 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
9U5U The 1:1 cryo-EM structure of BAP1/ASXL1-K351Ub in complex with H2AK119Ub nucleosome Deposited 2025-03-21 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
9XSF Cryo-EM structure of H4S47GlcNAc nucleosome at 3.39 angstrom Deposited 2025-11-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.39 Å
9ZEN Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1B2 Deposited 2025-11-30 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain D 34–126（93 aa）
Chain H 34–126（93 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES pH7.6, 50 mM NaCl, 0.5 mM MgCl2, 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.17 Å
9ZEO Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1G1 Deposited 2025-11-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain D 32–126（95 aa）
Chain H 32–126（95 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES pH7.6, 50 mM NaCl, 0.5 mM MgCl2, 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å

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

View Construct and Data Evidence
UniProt name H2B1K_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D； PDBConstruct 1–91； UniProt 35–125 Author chain H； PDBConstruct 1–91； UniProt 35–125

Histone H4

Homo sapiens

UniProt A0A8C2GGI7

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 10 DNA 2 PDB declaration: dodecameric（12） Consistent with all polymer counts Chain F； UniProt 11–91 Not recorded Histone H3 × 2 （A0A653DHJ5） Histone H4 (Fragment) × 1 （A0A093PN76） Histone H2A type 1-B/E × 1 （P04908） Histone H2B type 1-K × 2 （O60814） Histone H2A type 1-B/E × 1 （P04908） Protein SSX2 × 1 （Q16385） Polyubiquitin-B (Fragment) × 1 （J3QS39） DNA (137-MER) × 1 DNA (136-MER) × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.05 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name A0A8C2GGI7_CYPCA
Isoform —
PDB entities 5
Chains and sequence ranges Author chain F； PDBConstruct 1–81； UniProt 11–91

Protein SSX2

Homo sapiens

UniProt Q16385

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 10 DNA 2 PDB declaration: dodecameric（12） Consistent with all polymer counts Chain S； UniProt 162–184 Not recorded Histone H3 × 2 （A0A653DHJ5） Histone H4 (Fragment) × 1 （A0A093PN76） Histone H2A type 1-B/E × 1 （P04908） Histone H2B type 1-K × 2 （O60814） Histone H4 × 1 （A0A8C2GGI7） Histone H2A type 1-B/E × 1 （P04908） Polyubiquitin-B (Fragment) × 1 （J3QS39） DNA (137-MER) × 1 DNA (136-MER) × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.05 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name SSX2_HUMAN
Isoform —
PDB entities 7
Chains and sequence ranges Author chain S； PDBConstruct 1–23； UniProt 162–184

Polyubiquitin-B (Fragment)

Homo sapiens

UniProt J3QS39

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 10 DNA 2 PDB declaration: dodecameric（12） Consistent with all polymer counts Chain U； UniProt 1–74 Not recorded Histone H3 × 2 （A0A653DHJ5） Histone H4 (Fragment) × 1 （A0A093PN76） Histone H2A type 1-B/E × 1 （P04908） Histone H2B type 1-K × 2 （O60814） Histone H4 × 1 （A0A8C2GGI7） Histone H2A type 1-B/E × 1 （P04908） Protein SSX2 × 1 （Q16385） DNA (137-MER) × 1 DNA (136-MER) × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.05 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 8HQY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2DEN Solution Structure of the Ubiquitin-Associated Domain of Human BMSC-UbP and its Complex with Ubiquitin Deposited 2006-02-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Pressure ambient
NMR sample composition 1mM HGB1-UBA | 20mM phosphate, 100mM NaCl, pH6.5
NMR sample composition 1mM Ubiquitin | 20mM phosphate, 100mM NaCl, pH6.5
Resolution not provided
2MBH NMR structure of EKLF(22-40)/Ubiquitin Complex Deposited 2013-07-31 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 20
NMR sample composition 4 mM Ubi_unl, 0.8 mM [U-100% 15N] EKLF, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 4 mM EKLF_unl, 0.8 mM [U-100% 15N] Ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 4 mM EKLF_unl, 0.8 mM [U-100% 13C; U-100% 15N] Ubiquitin, 100% D2O | 100% D2O
NMR sample composition 4 mM Ubi_unl, 0.8 mM [U-100% 13C; U-100% 15N] EKLF, 100% D2O | 100% D2O
Resolution not provided
3PRM Structural analysis of a viral OTU domain protease from the Crimean-Congo Hemorrhagic Fever virus in complex with human ubiquitin Deposited 2010-11-30 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；22-26% PEG 8000, 0.1 M Na cacodylate, 0.2 M Mg acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.30 Å R-free 0.267
3PRM Structural analysis of a viral OTU domain protease from the Crimean-Congo Hemorrhagic Fever virus in complex with human ubiquitin Deposited 2010-11-30 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 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；22-26% PEG 8000, 0.1 M Na cacodylate, 0.2 M Mg acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.30 Å R-free 0.267
3PRP Structural analysis of a viral OTU domain protease from the Crimean-Congo Hemorrhagic Fever virus in complex with human ubiquitin Deposited 2010-11-30 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；22-28% PEG 8000, 100 mM Na cacodylate pH 6.5, 100-250 mM Mg acetate, and 2% n-Octyl- -D-glucoside, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.70 Å R-free 0.212
3PRP Structural analysis of a viral OTU domain protease from the Crimean-Congo Hemorrhagic Fever virus in complex with human ubiquitin Deposited 2010-11-30 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 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；22-28% PEG 8000, 100 mM Na cacodylate pH 6.5, 100-250 mM Mg acetate, and 2% n-Octyl- -D-glucoside, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.70 Å R-free 0.212
5TXK CRYSTAL STRUCTURE OF USP35 C450S IN COMPLEX WITH UBIQUITIN Deposited 2016-11-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded SO4 SULFATE ION × 3 EDO 1,2-ETHANEDIOL × 3 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；296 K；0.95 M ammonium sulphate 0.1 M HEPES
Resolution 1.84 Å R-free 0.183
5YDR Structure of DNMT1 RFTS domain in complex with ubiquitin Deposited 2017-09-14 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 × 3 PDB declaration: trimeric
Chain A 1–73（73 aa） Fragment：UNP residues 1-73
Chain D 1–73（73 aa） Fragment：UNP residues 1-73
Not recorded PO4 PHOSPHATE ION × 2 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8；291 K；20mM Tris-HCl, 200mM sodium acetate, 25% PEG 4000
Resolution 2.00 Å R-free 0.233
6K4I The partially disordered conformation of ubiquitin (Q41N variant) Deposited 2019-05-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Mutation：Q41N No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4；278 K；Ionic strength (raw mmCIF value) 30；Pressure 2500
NMR sample composition 1.0 mM [U-99% 13C; U-99% 15N] ubiquitin, 30 mM D D-acetate, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.3 mM [U-99% 15N] ubiquitin, 30 mM D D-acetate, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6KOW Retracted state of S65/T66 double-phosphorylated ubiquitin Deposited 2019-08-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 150；Pressure 760
NMR sample composition 20 mM HEPES, 150 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6KOX Relaxed state of S65/T66 double-phosphorylated ubiquitin Deposited 2019-08-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 150；Pressure 760
NMR sample composition 20 mM HEPES, 150 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6NJG Ubiquitin Variant in Complex with Ubiquitin Interacting Motif Deposited 2019-01-03 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 C 1–78（78 aa）
Mutation：K6Q, L8I, G10V, K11M, T12R, T14A, K48M, Q62K, K63R, E64D, T66N, H68Y, L71S, R72S, G75S, G76L, M77R, Q78A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.1 M DL-Malic acid
Resolution 2.35 Å R-free 0.244
6NOG Poised-state Dot1L bound to the H2B-Ubiquitinated nucleosome Deposited 2019-01-16 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain L 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use.
cryo-EM vitrification conditions Cryogen ETHANE；Blot once for 3.5 seconds before freezing
Resolution 3.90 Å
6O96 Dot1L bound to the H2BK120 Ubiquitinated nucleosome Deposited 2019-03-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain L 1–76（76 aa）
Mutation：G76C SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen PROPANE；blotted for 3s before plunging
Resolution 3.50 Å
6OAM Crystal Structure of ChlaDUB2 DUB domain Deposited 2019-03-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES sodium pH 7.5, 0.8 M sodium phosphate monobasic monohydrate, 0.8 M sodium phosphate monobasic, 0.1M Cesium chloride
Resolution 2.50 Å R-free 0.306
6OAM Crystal Structure of ChlaDUB2 DUB domain Deposited 2019-03-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES sodium pH 7.5, 0.8 M sodium phosphate monobasic monohydrate, 0.8 M sodium phosphate monobasic, 0.1M Cesium chloride
Resolution 2.50 Å R-free 0.306
6PZV Crystal Structure of Bovine DNMT1 RFTS domain in complex with H3K9me3 and Ubiquitin Deposited 2019-08-01 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 A 1–76（76 aa）
Chain B 1–76（76 aa）
Not recorded FLC CITRATE ANION × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.5；277 K；0.1M citric acid (pH 3.5), 28% PEG8000
Resolution 3.01 Å R-free 0.272
6PZV Crystal Structure of Bovine DNMT1 RFTS domain in complex with H3K9me3 and Ubiquitin Deposited 2019-08-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 1–76（76 aa）
Chain F 1–76（76 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.5；277 K；0.1M citric acid (pH 3.5), 28% PEG8000
Resolution 3.01 Å R-free 0.272
6QF8 Solution NMR ensemble for human ubiquitin at 298K compiled using the CoMAND method Deposited 2019-01-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.8；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1
NMR sample composition 1.0 mM [U-99% 13C; U-99% 15N] human ubiquitin, 40 mM sodium phosphate, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
6TBM Structure of SAGA bound to TBP, including Spt8 and DUB Deposited 2019-11-01 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain R 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 20.00 Å
6UH5 Structural basis of COMPASS eCM recognition of the H2Bub nucleosome Deposited 2019-09-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain Q 1–76（76 aa）
Mutation：G76C ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6XAA SARS CoV-2 PLpro in complex with ubiquitin propargylamide Deposited 2020-06-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Mutation：G76 replaced with propargylamide Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；30% PEG4000, 0.2 M sodium acetate, 0.1 M Tris chloride, pH 8.5
Resolution 2.70 Å R-free 0.260
6XQC UbKEKS Deposited 2020-07-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1
NMR sample composition 500 uM [U-13C; U-15N] UbKEKS, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 500 uM [U-13C; U-15N] UbKEKS, 100% D2O | 100% D2O
Resolution not provided
7BBD Crystal structure of monoubiquitinated TRIM21 RING (Ub-RING) In complex with ubiquitin charged Ube2N (Ube2N~Ub) and Ube2V2 Deposited 2020-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–74（74 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290.15 K；MOPSO, Bis-Tris, PEG 4K, 1,2,6-hexanetriol, Li, Na, K
Resolution 2.20 Å R-free 0.252
7BU0 Crystal structure of a OTU deubiquitinase in complex with Ub-PA Deposited 2020-04-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–75（75 aa）
Chain D 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289.15 K；0.1M Magnesium formate dihydrate 15% w/v PEG 3350
Resolution 2.43 Å R-free 0.255
7E8I Structural insight into BRCA1-BARD1 complex recruitment to damaged chromatin Deposited 2021-03-01 Different construct Different mutation/modification Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain L 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7NBB Branched Lys48- and Lys63-linked tri-ubiquitin (K48-K63-Ub3) in complex with synthetic nanobody NbSL3 Deposited 2021-01-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–72（72 aa）
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Mutation：K48R K63R Mutation：K48R K63R MG MAGNESIUM ION × 4 GOL GLYCEROL × 1 CL CHLORIDE ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；277.15 K；0.1 M Bis-Tris pH 7.2 0.28 M MgCl2 21% PEG3350 0.15 M NaCl 0.05 M Tris/HCl pH 7.5
Resolution 1.55 Å R-free 0.212
7NBB Branched Lys48- and Lys63-linked tri-ubiquitin (K48-K63-Ub3) in complex with synthetic nanobody NbSL3 Deposited 2021-01-26 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 × 4 PDB declaration: tetrameric
Chain E 1–72（72 aa）
Chain F 1–76（76 aa）
Chain G 1–76（76 aa）
Mutation：K48R K63R Mutation：K48R K63R MG MAGNESIUM ION × 3 GOL GLYCEROL × 1 CL CHLORIDE ION × 5 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；277.15 K；0.1 M Bis-Tris pH 7.2 0.28 M MgCl2 21% PEG3350 0.15 M NaCl 0.05 M Tris/HCl pH 7.5
Resolution 1.55 Å R-free 0.212
7NPO Branched K48-K63-Ub3 Deposited 2021-02-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–72（72 aa）
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Mutation：K48R K63R Mutation：K48R K63R GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M Ammonium acetate, 20 mM Tris pH 7.5, 50 mM NaCl, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v PEG 4000; 22 mg/ml
Resolution 2.19 Å R-free 0.284
7QO4 26S proteasome WT-Ubp6-UbVS complex in the si state (ATPases, Rpn1, Ubp6, and UbVS) Deposited 2021-12-23 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 9 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ATP ADENOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å
7QO6 26S proteasome Rpt1-RK -Ubp6-UbVS complex in the s2 state Deposited 2021-12-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain 9 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ATP ADENOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.30 Å
7UD5 Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome Deposited 2022-03-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain O 1–76（76 aa）
Mutation：G76C SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
7US1 Structure of parkin (R0RB) bound to two phospho-ubiquitin molecules Deposited 2022-04-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–74（74 aa）
Chain C 1–74（74 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 6 PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277.15 K；0.1M Bis-Tris propane pH 7.5, 20.5% PEG3350, 0.2M NaI
Resolution 2.48 Å R-free 0.258
7W3U USP34 catalytic domain in complex with UbPA Deposited 2021-11-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；15% w/v PEG 3350, 0.8M Magnesium chloride hexahydrate, 0.6mM Lyso PG, 1 mM Facade R-EPC
Resolution 3.13 Å R-free 0.245
7W3U USP34 catalytic domain in complex with UbPA Deposited 2021-11-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–75（75 aa）
Not recorded ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；15% w/v PEG 3350, 0.8M Magnesium chloride hexahydrate, 0.6mM Lyso PG, 1 mM Facade R-EPC
Resolution 3.13 Å R-free 0.245
7W3U USP34 catalytic domain in complex with UbPA Deposited 2021-11-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–75（75 aa）
Not recorded ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；15% w/v PEG 3350, 0.8M Magnesium chloride hexahydrate, 0.6mM Lyso PG, 1 mM Facade R-EPC
Resolution 3.13 Å R-free 0.245
7W54 Crystal structure of a bacterial OTU DUB with Ub-PA Deposited 2021-11-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–75（75 aa）
Chain D 1–75（75 aa）
Chain E 1–75（75 aa）
Chain F 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；299 K；100 mM Magnesium formate, 15% (w/v) PEG 3350, pH 8.0
Resolution 2.64 Å R-free 0.253
7YQK cryo-EM structure of gammaH2AXK15ub-H4K20me2 nucleosome bound to 53BP1 Deposited 2022-08-07 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain O 1–75（75 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
8A67 Branched Lys48- and Lys63-linked tri-ubiquitin (K48-K63-Ub3) in complex with matured synthetic nanobody NbSL3.3Q (3rd generation) Deposited 2022-06-16 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 × 4 PDB declaration: tetrameric
Chain A 1–72（72 aa）
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Mutation：K48R K63R Mutation：K48R K63R GOL GLYCEROL × 1 IPA ISOPROPYL ALCOHOL × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；Protein concentrated to 14.5 mg/ml in 20 mM HEPES pH 7.5, 150 mM NaCl. Mixed 200 nl protein with 100 nl mother liquor (0.1 M HEPES pH 7.5, 10% 2-propanol, 20% PEG4000). Crystals harvested and cryo-protected with Mother liquor supplemented with 30% glycerol.
Resolution 1.86 Å R-free 0.245
8A67 Branched Lys48- and Lys63-linked tri-ubiquitin (K48-K63-Ub3) in complex with matured synthetic nanobody NbSL3.3Q (3rd generation) Deposited 2022-06-16 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 × 4 PDB declaration: tetrameric
Chain E 1–72（72 aa）
Chain F 1–76（76 aa）
Chain G 1–76（76 aa）
Mutation：K48R K63R Mutation：K48R K63R GOL GLYCEROL × 1 IPA ISOPROPYL ALCOHOL × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；Protein concentrated to 14.5 mg/ml in 20 mM HEPES pH 7.5, 150 mM NaCl. Mixed 200 nl protein with 100 nl mother liquor (0.1 M HEPES pH 7.5, 10% 2-propanol, 20% PEG4000). Crystals harvested and cryo-protected with Mother liquor supplemented with 30% glycerol.
Resolution 1.86 Å R-free 0.245
8DU4 Complex between RbBP5-WDR5 and an H2B-ubiquitinated nucleosome Deposited 2022-07-26 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain O 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
8K6E LnaB-Actin-PRUb ternary complex Deposited 2023-07-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–75（75 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；289 K；PEG 8000; Sodium chloride; Sodium HEPES
Resolution 2.74 Å R-free 0.245
8T2D Ubiquitin variant i53:Mutant T12Y.T14E.L67R with 53BP1 Tudor domain Deposited 2023-06-05 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 1–74（74 aa）
Mutation：T12Y, T14E, L67R No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290 K；0.1 M MES pH 6.0, 0.2 M Trimethylamine N-oxide dehydrate, 13% w/v PEG MME 2000
Resolution 1.75 Å R-free 0.273
8WG5 Cryo-EM structure of USP16 bound to H2AK119Ub nucleosome Deposited 2023-09-20 Different construct Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain U 1–75（75 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
9KQO cryo-EM structure of RNF20/RNF40-RAD6A-Ub in complex with H2BS112GlcNAc nucleosome Deposited 2024-11-26 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–75（75 aa）
Not recorded ZN ZINC ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.48 Å
9NY4 USP21 bound to H2AK119ub nucleosome Deposited 2025-03-26 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain U 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å

38 other PDB entries and 46 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name J3QS39_HUMAN
Isoform —
PDB entities 8
Chains and sequence ranges Author chain U； PDBConstruct 1–74； UniProt 1–74

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

SAXS scattering curve SAXS Profile

SAXS profile for 8hqy

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8hqy
Deposition date deposition_date2022-12-14
Structure title titleCryo-EM structure of SSX1 bound to the H2AK119Ub nucleosome at a resolution of 3.05 angstrom
Keywords keywordsSSX1, H2AK119Ub nucleosome, Synovial Sarcoma, ssBAF, reader protein, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier40.26 Å
Radius of gyration Rg (electron density) rg_electron37.66 Å
Forward intensity I(0) i0831521000.00
Molecular weight molecular_weight179880.0 kDa
Excluded volume excluded_volume201800 ų
Envelope volume envelope_volume302340 ų
Hydration-shell volume shell_volume65063 ų
Envelope diameter envelope_diameter127.7 Å
Shell Rg shell_rg45.38 Å
Envelope Rg envelope_rg36.97 Å
Shape Rg shape_rg37.48 Å
Total Rg total_rg38.40 Å
Total atoms total_atoms12301
Residues n_residues1119
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax121.7 Å
Rg (real space) rg_real40.07 Å
Rg uncertainty (real space) rg_real_error0.77 Å
I(0) (real space) i0_real8.3150e+08
I(0) uncertainty (real space) i0_real_error1.2900e+07
Rg (reciprocal space) rg_reciprocal40.26 Å
I(0) (reciprocal space) i0_reciprocal831700000.0000
Solution quality estimate total_estimate0.9033
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks0
Primary peak position r_peak_primary— Å
Skewness Skewness skewness0.095
Kurtosis Kurtosis kurtosis-0.599
Angular range angular_range— – 0.1950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha48750000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.958; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.888
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (10)

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8. Citations (1)

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9. Files and Curves (10)