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7bqz

Crystal Structure of Spindlin1 bound to H3(K4me3-K9me3) peptide

Method: X-RAY DIFFRACTION Dmax: 118.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Spindlin-1

Homo sapiens

UniProt Q9Y657

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 45–262 Not recorded H3(K4me3-K9me3) peptide × 1 （Q71DI3） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；291 K；2.8M sodium acetate, pH7.0 Resolution 3.10 Å R-free 0.264
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 45–262 Not recorded H3(K4me3-K9me3) peptide × 1 （Q71DI3） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；291 K；2.8M sodium acetate, pH7.0 Resolution 3.10 Å R-free 0.264
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain E； UniProt 45–262 Not recorded H3(K4me3-K9me3) peptide × 1 （Q71DI3） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；291 K；2.8M sodium acetate, pH7.0 Resolution 3.10 Å R-free 0.264
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain G； UniProt 45–262 Not recorded H3(K4me3-K9me3) peptide × 1 （Q71DI3） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；291 K；2.8M sodium acetate, pH7.0 Resolution 3.10 Å R-free 0.264

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 7BQZ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2NS2 Crystal Structure of Spindlin1 Deposited 2006-11-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 26–262（237 aa） Fragment：residues 1-237 (26-262)
Chain B 26–262（237 aa） Fragment：residues 1-237 (26-262)
Not recorded PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；288 K；Ammonium Sulfate, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 2.20 Å R-free 0.260
4H75 Crystal structure of human Spindlin1 in complex with a histone H3K4(me3) peptide Deposited 2012-09-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 27–262（236 aa） Fragment：UNP residues 27-262
Not recorded GOL GLYCEROL × 1 SO4 SULFATE ION × 3 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；289 K；0.1 M CHES, pH 9.5, 2.1 M ammonium sulfate, 0.2 M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.10 Å R-free 0.218
4MZF Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2a) peptide Deposited 2013-09-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 50–262（213 aa） Fragment：UNP residues 50-262
Not recorded CL CHLORIDE ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291.15 K；20% PEG 8000, 20% PEG 400, 0.1M MgCl2, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K
Resolution 2.10 Å R-free 0.255
4MZG Crystal structure of human Spindlin1 bound to histone H3K4me3 peptide Deposited 2013-09-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 50–262（213 aa） Fragment：UNP residues 50-262
Not recorded MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291.15 K；37.5% MPD_P1K_P3350, 0.1M bicine/Trizma, pH 8.5, 0.06M MgCl2/CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K
Resolution 1.70 Å R-free 0.207
4MZG Crystal structure of human Spindlin1 bound to histone H3K4me3 peptide Deposited 2013-09-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 50–262（213 aa） Fragment：UNP residues 50-262
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291.15 K；37.5% MPD_P1K_P3350, 0.1M bicine/Trizma, pH 8.5, 0.06M MgCl2/CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K
Resolution 1.70 Å R-free 0.207
4MZH Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2s) peptide Deposited 2013-09-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 50–262（213 aa） Fragment：UNP residues 50-262
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291.15 K；20% PEG 8000, 20% PEG 400, 0.1M MgCl2, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K
Resolution 2.20 Å R-free 0.247
5JSG Crystal structure of Spindlin1 bound to compound EML405 Deposited 2016-05-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 50–262（213 aa） Fragment：Spin/Ssty Repeats, UNP residues 50-262
Not recorded 6P9 [2-(phenylamino)-1,4-phenylene]bis({4-[2-(pyrrolidin-1-yl)ethyl]piperidin-1-yl}methanone) × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.2M MgCl2, 0.1M HepesNa, 20% PEG 10000
Resolution 2.50 Å R-free 0.245
5JSG Crystal structure of Spindlin1 bound to compound EML405 Deposited 2016-05-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 50–262（213 aa） Fragment：Spin/Ssty Repeats, UNP residues 50-262
Not recorded 6P9 [2-(phenylamino)-1,4-phenylene]bis({4-[2-(pyrrolidin-1-yl)ethyl]piperidin-1-yl}methanone) × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.2M MgCl2, 0.1M HepesNa, 20% PEG 10000
Resolution 2.50 Å R-free 0.245
5JSJ Crystal structure of Spindlin1 bound to compound EML631 Deposited 2016-05-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 50–262（213 aa） Fragment：Spin/Ssty Repeats, UNP residues 50-262
Not recorded 6PD [4-(2-pyrrolidin-1-ylethyl)piperidin-1-yl]-[4-[4-(2-pyrrolidin-1-ylethyl)piperidin-1-yl]carbonyl-3-[[4-(pyrrolidin-1-ylmethoxy)phenyl]amino]phenyl]methanone × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.2M MgCl2, 0.1M HepesNa, 25% PEG 3350
Resolution 2.35 Å R-free 0.249
5JSJ Crystal structure of Spindlin1 bound to compound EML631 Deposited 2016-05-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 50–262（213 aa） Fragment：Spin/Ssty Repeats, UNP residues 50-262
Not recorded 6PD [4-(2-pyrrolidin-1-ylethyl)piperidin-1-yl]-[4-[4-(2-pyrrolidin-1-ylethyl)piperidin-1-yl]carbonyl-3-[[4-(pyrrolidin-1-ylmethoxy)phenyl]amino]phenyl]methanone × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.2M MgCl2, 0.1M HepesNa, 25% PEG 3350
Resolution 2.35 Å R-free 0.249
5Y5W Crystal structure of human Spindlin1 in complex with a histone H4K20(me3) peptide Deposited 2017-08-10 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 51–262（212 aa） Fragment：UNP residues 51-262
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；1.5 M (NH4)2SO4, 0.1 M Bis-Tris
Resolution 3.30 Å R-free 0.308
5Y5W Crystal structure of human Spindlin1 in complex with a histone H4K20(me3) peptide Deposited 2017-08-10 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 51–262（212 aa） Fragment：UNP residues 51-262
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；1.5 M (NH4)2SO4, 0.1 M Bis-Tris
Resolution 3.30 Å R-free 0.308
5Y5W Crystal structure of human Spindlin1 in complex with a histone H4K20(me3) peptide Deposited 2017-08-10 Different construct Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 51–262（212 aa） Fragment：UNP residues 51-262
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；1.5 M (NH4)2SO4, 0.1 M Bis-Tris
Resolution 3.30 Å R-free 0.308
5Y5W Crystal structure of human Spindlin1 in complex with a histone H4K20(me3) peptide Deposited 2017-08-10 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 51–262（212 aa） Fragment：UNP residues 51-262
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；1.5 M (NH4)2SO4, 0.1 M Bis-Tris
Resolution 3.30 Å R-free 0.308
6I8B Crystal structure of Spindlin1 in complex with the inhibitor VinSpinIn Deposited 2018-11-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 49–262（214 aa）
Not recorded H7T 2-[4-[2-[[2-[3-[2-azanyl-5-(cyclopropylmethoxy)-3,3-dimethyl-indol-6-yl]oxypropyl]-1,3-dihydroisoindol-5-yl]oxy]ethyl]-1,2,3-triazol-1-yl]-1-[4-(2-pyrrolidin-1-ylethyl)piperidin-1-yl]ethanone × 1 DMS DIMETHYL SULFOXIDE × 4 GLY GLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；55% MPD and 0.1 M SPG buffer pH 5.5
Resolution 1.76 Å R-free 0.254
6I8B Crystal structure of Spindlin1 in complex with the inhibitor VinSpinIn Deposited 2018-11-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 49–262（214 aa）
Not recorded H7T 2-[4-[2-[[2-[3-[2-azanyl-5-(cyclopropylmethoxy)-3,3-dimethyl-indol-6-yl]oxypropyl]-1,3-dihydroisoindol-5-yl]oxy]ethyl]-1,2,3-triazol-1-yl]-1-[4-(2-pyrrolidin-1-ylethyl)piperidin-1-yl]ethanone × 1 DMS DIMETHYL SULFOXIDE × 1 GLY GLYCINE × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；55% MPD and 0.1 M SPG buffer pH 5.5
Resolution 1.76 Å R-free 0.254
6I8L Crystal structure of Spindlin1 in complex with the inhibitor TD001851a Deposited 2018-11-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 49–262（214 aa）
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 DMS DIMETHYL SULFOXIDE × 1 H7Q 5'-(cyclopropylmethoxy)-6'-[3-(1,3-dihydroisoindol-2-yl)propoxy]spiro[cyclopentane-1,3'-indole]-2'-amine × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；55% MPD and 0.1 M SPG buffer
Resolution 1.58 Å R-free 0.207
6I8Y Crystal structure of Spindlin1 in complex with the Methyltransferase inhibitor A366 Deposited 2018-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 49–262（214 aa）
Not recorded 2OD 5'-methoxy-6'-[3-(pyrrolidin-1-yl)propoxy]spiro[cyclobutane-1,3'-indol]-2'-amine × 2 EDO 1,2-ETHANEDIOL × 2 DMS DIMETHYL SULFOXIDE × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 GOL GLYCEROL × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1M Bis-Tris pH=6.5,0.2M CaCl2, 45% MPD
Resolution 1.52 Å R-free 0.205
6QPL Crystal structure of Spindlin1 in complex with the inhibitor MS31 Deposited 2019-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 49–262（214 aa）
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 DMS DIMETHYL SULFOXIDE × 2 JC5 [3-(aminomethyl)-5-[3-(1,3-dihydroisoindol-2-yl)propoxy]-4-methoxy-phenyl]methanamine × 1 GLY GLYCINE × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；60% MPD and 0.1 M SPG buffer pH 6.0
Resolution 1.60 Å R-free 0.208
7BU9 Crystal Structure of Spindlin1-H3(K4me3-K9me2) complex Deposited 2020-04-05 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 45–262（218 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；3.6M sodium formate, 3% DMSO
Resolution 3.50 Å R-free 0.264
7BU9 Crystal Structure of Spindlin1-H3(K4me3-K9me2) complex Deposited 2020-04-05 Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 45–262（218 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；3.6M sodium formate, 3% DMSO
Resolution 3.50 Å R-free 0.264
7BU9 Crystal Structure of Spindlin1-H3(K4me3-K9me2) complex Deposited 2020-04-05 Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 45–262（218 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；3.6M sodium formate, 3% DMSO
Resolution 3.50 Å R-free 0.264
7BU9 Crystal Structure of Spindlin1-H3(K4me3-K9me2) complex Deposited 2020-04-05 Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 45–262（218 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；3.6M sodium formate, 3% DMSO
Resolution 3.50 Å R-free 0.264
7CNA Crystal structure of Spindlin1/C11orf84 complex bound to histone H3K4me3K9me3 peptide Deposited 2020-07-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 51–262（212 aa）
Chain D 51–262（212 aa）
Not recorded BEN BENZAMIDINE × 6 CL CHLORIDE ION × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1 M sodium cacodylate pH 6.5, 35% PEG3350, 5% glycerol, 2% Benzamidine hydrochloride
Resolution 1.60 Å R-free 0.201
7E9M Crystal Structure of Spindlin1 bound to SPINDOC Docpep3 Deposited 2021-03-04 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–262（262 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；291 K；0.2M magnesium acetate, 0.1M Sodium cacodylate pH 6.5, 20% PEG 8000
Resolution 2.50 Å R-free 0.253
7E9M Crystal Structure of Spindlin1 bound to SPINDOC Docpep3 Deposited 2021-03-04 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–262（262 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；291 K；0.2M magnesium acetate, 0.1M Sodium cacodylate pH 6.5, 20% PEG 8000
Resolution 2.50 Å R-free 0.253
7EA1 Crystal Structure of Spindlin1 bound to SPINDOC Docpep2 Deposited 2021-03-05 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 50–262（213 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；291 K；0.1M Sodium chloride, 0.1M BIS-TRIS pH 6.5, 1.5M Ammonium sulfate
Resolution 2.70 Å R-free 0.286
7EA1 Crystal Structure of Spindlin1 bound to SPINDOC Docpep2 Deposited 2021-03-05 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 50–262（213 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；291 K；0.1M Sodium chloride, 0.1M BIS-TRIS pH 6.5, 1.5M Ammonium sulfate
Resolution 2.70 Å R-free 0.286
7OCB Crystal structure of Spindlin1 in complex with the inhibitor XY49-92B Deposited 2021-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 49–262（214 aa）
Not recorded V88 7-[3-(1,3-dihydroisoindol-2-yl)propoxy]-2N-[2-(dimethylamino)ethyl]-6-methoxy-4N-(1-propan-2-ylpiperidin-4-yl)quinazoline-2,4-diamine × 1 PO4 PHOSPHATE ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 CL CHLORIDE ION × 1 GLY GLYCINE × 1 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；55-60 % MPD and 0.1 M SPG buffer pH 5.5-6.0
Resolution 1.42 Å R-free 0.206
8GTX Crystal Structure of human Spindlin1-HBx complex Deposited 2022-09-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 50–262（213 aa）
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；16%(w/v) PEG 8000, 0.04M Potassium phosphate dibasic, 20% (v/v) Glycerol
Resolution 1.80 Å R-free 0.197
9T2Z Spindlin 1 with crystallization epitope mutations H127D:L128D:T131R Deposited 2025-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 49–262（214 aa）
Mutation：H127D:L128D:T131R EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277.15 K；0.2M ammonium sulfate 25% PEG3350 0.1M HEPES pH 7.5
Resolution 1.87 Å R-free 0.288

19 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPIN1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–220； UniProt 45–262 Author chain C； PDBConstruct 3–220； UniProt 45–262 Author chain E； PDBConstruct 3–220； UniProt 45–262 Author chain G； PDBConstruct 3–220； UniProt 45–262

H3(K4me3-K9me3) peptide

OrganismNot specified

UniProt Q71DI3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 2–16 Non-standard monomer：Yes (specific site not provided by mmCIF) Spindlin-1 × 1 （Q9Y657） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；291 K；2.8M sodium acetate, pH7.0 Resolution 3.10 Å R-free 0.264
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 2–16 Non-standard monomer：Yes (specific site not provided by mmCIF) Spindlin-1 × 1 （Q9Y657） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；291 K；2.8M sodium acetate, pH7.0 Resolution 3.10 Å R-free 0.264
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain F； UniProt 2–16 Non-standard monomer：Yes (specific site not provided by mmCIF) Spindlin-1 × 1 （Q9Y657） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；291 K；2.8M sodium acetate, pH7.0 Resolution 3.10 Å R-free 0.264
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain H； UniProt 2–16 Non-standard monomer：Yes (specific site not provided by mmCIF) Spindlin-1 × 1 （Q9Y657） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；291 K；2.8M sodium acetate, pH7.0 Resolution 3.10 Å R-free 0.264

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 7BQZ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
10XZ Non-damaged nucleosome Deposited 2026-02-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
10YA Nucleosome containing a nick at SHL-4 Deposited 2026-02-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
10YB Nucleosome containing a nick at SHL-2 Deposited 2026-02-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
10YC Nucleosome containing a nick at SHL-4 Deposited 2026-02-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
10YD Nucleosome containing a nick at SHL-6 Deposited 2026-02-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
10YE DNA Ligase IIIa bound to nucleosome containing a nick at SHL0 Deposited 2026-02-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain A 39–135（97 aa）
Chain E 39–135（97 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
10YF DNA Ligase IIIa bound to nucleosome containing a nick at SHL-2 (composite) Deposited 2026-02-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain A 39–134（96 aa）
Chain E 39–134（96 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution not provided
10YG DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-4 (composite) Deposited 2026-02-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain A 39–135（97 aa）
Chain E 39–135（97 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution not provided
10YH DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-6 (composite) Deposited 2026-02-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain A 39–135（97 aa）
Chain E 39–135（97 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
10YI XRCC1-DNA Ligase IIIa complex bound to a nucleosome containing a nick at SHL-6 (composite) Deposited 2026-02-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain A 39–135（97 aa）
Chain E 39–135（97 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
2X4W Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1. Deposited 2010-02-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 23–43（21 aa） Fragment：RESIDUES 23-43
Non-standard monomer：Yes (specific site not provided by mmCIF) FMT FORMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；4M SODIUM FORMATE, 0.1M TRIS (PH 8.5), 0.01M NACL
Resolution 1.50 Å R-free 0.216
2X4X Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1. Deposited 2010-02-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 23–43（21 aa） Fragment：RESIDUES 23-43
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；20% PEG3350, 0.2M LITHIUM SULPHATE, 0.1M TRIS (PH 8.5) 0.01M NACL
Resolution 1.85 Å R-free 0.239
2X4X Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1. Deposited 2010-02-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 23–43（21 aa） Fragment：RESIDUES 23-43
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；20% PEG3350, 0.2M LITHIUM SULPHATE, 0.1M TRIS (PH 8.5) 0.01M NACL
Resolution 1.85 Å R-free 0.239
2X4X Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1. Deposited 2010-02-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 23–43（21 aa） Fragment：RESIDUES 23-43
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；20% PEG3350, 0.2M LITHIUM SULPHATE, 0.1M TRIS (PH 8.5) 0.01M NACL
Resolution 1.85 Å R-free 0.239
2X4X Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1. Deposited 2010-02-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 23–43（21 aa） Fragment：RESIDUES 23-43
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；20% PEG3350, 0.2M LITHIUM SULPHATE, 0.1M TRIS (PH 8.5) 0.01M NACL
Resolution 1.85 Å R-free 0.239
2X4Y Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1. Deposited 2010-02-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 23–43（21 aa） Fragment：RESIDUES 23-43
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；30% PEG4K, 0.2M LITHIUM SULPHATE, 0.1M TRIS (PH 8.5), 0.01M NACL.
Resolution 1.70 Å R-free 0.227
2X4Y Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1. Deposited 2010-02-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 23–43（21 aa） Fragment：RESIDUES 23-43
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；30% PEG4K, 0.2M LITHIUM SULPHATE, 0.1M TRIS (PH 8.5), 0.01M NACL.
Resolution 1.70 Å R-free 0.227
2X4Y Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1. Deposited 2010-02-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 23–43（21 aa） Fragment：RESIDUES 23-43
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；30% PEG4K, 0.2M LITHIUM SULPHATE, 0.1M TRIS (PH 8.5), 0.01M NACL.
Resolution 1.70 Å R-free 0.227
2X4Y Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1. Deposited 2010-02-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 23–43（21 aa） Fragment：RESIDUES 23-43
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；30% PEG4K, 0.2M LITHIUM SULPHATE, 0.1M TRIS (PH 8.5), 0.01M NACL.
Resolution 1.70 Å R-free 0.227
2X4Y Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1. Deposited 2010-02-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 23–43（21 aa） Fragment：RESIDUES 23-43
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；30% PEG4K, 0.2M LITHIUM SULPHATE, 0.1M TRIS (PH 8.5), 0.01M NACL.
Resolution 1.70 Å R-free 0.227
2X4Y Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1. Deposited 2010-02-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain N 23–43（21 aa） Fragment：RESIDUES 23-43
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；30% PEG4K, 0.2M LITHIUM SULPHATE, 0.1M TRIS (PH 8.5), 0.01M NACL.
Resolution 1.70 Å R-free 0.227
2X4Y Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1. Deposited 2010-02-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain J 23–43（21 aa） Fragment：RESIDUES 23-43
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；30% PEG4K, 0.2M LITHIUM SULPHATE, 0.1M TRIS (PH 8.5), 0.01M NACL.
Resolution 1.70 Å R-free 0.227
2X4Y Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1. Deposited 2010-02-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 23–43（21 aa） Fragment：RESIDUES 23-43
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；30% PEG4K, 0.2M LITHIUM SULPHATE, 0.1M TRIS (PH 8.5), 0.01M NACL.
Resolution 1.70 Å R-free 0.227
3AV1 The human nucleosome structure containing the histone variant H3.2 Deposited 2011-02-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.290
3DB3 Crystal structure of the tandem tudor domains of the E3 ubiquitin-protein ligase UHRF1 in complex with trimethylated histone H3-K9 peptide Deposited 2008-05-30 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 7–12（6 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；3 M SODIUM FORMATE, 0.1 M SODIUM ACETATE, pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.282
3MO8 PWWP Domain of Human Bromodomain and PHD finger-containing protein 1 In Complex with Trimethylated H3K36 Peptide Deposited 2010-04-22 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 31–42（12 aa） Fragment：UNP residue 31-42
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；3.5M sodium formate, 0.1M Tris-HCl pH8.5, H3K36me3 peptide, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.69 Å R-free 0.207
4MZF Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2a) peptide Deposited 2013-09-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–10（9 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291.15 K；20% PEG 8000, 20% PEG 400, 0.1M MgCl2, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K
Resolution 2.10 Å R-free 0.255
4MZG Crystal structure of human Spindlin1 bound to histone H3K4me3 peptide Deposited 2013-09-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–21（20 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291.15 K；37.5% MPD_P1K_P3350, 0.1M bicine/Trizma, pH 8.5, 0.06M MgCl2/CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K
Resolution 1.70 Å R-free 0.207
4MZG Crystal structure of human Spindlin1 bound to histone H3K4me3 peptide Deposited 2013-09-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–21（20 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291.15 K；37.5% MPD_P1K_P3350, 0.1M bicine/Trizma, pH 8.5, 0.06M MgCl2/CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K
Resolution 1.70 Å R-free 0.207
4MZH Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2s) peptide Deposited 2013-09-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–10（9 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291.15 K；20% PEG 8000, 20% PEG 400, 0.1M MgCl2, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K
Resolution 2.20 Å R-free 0.247
4OUC Structure of human haspin in complex with histone H3 substrate Deposited 2014-02-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–13（12 aa） Fragment：histone H3 tail, UNP residues 2-13
Not recorded NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 6 5ID (2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL × 1 IOD IODIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277.15 K；20% PEG 3350, 0.2M potassium thiocyanate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Resolution 1.90 Å R-free 0.211
5B0Y Crystal structure of the nucleosome containing histone H3 with the crotonylated lysine 122 Deposited 2015-11-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.56 Å R-free 0.249
5B0Z The crystal structure of the nucleosome containing H3.2, at 1.98 A resolution Deposited 2015-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 1.99 Å R-free 0.254
5B40 The nucleosome structure containing H2B-K120 and H4-K31 monoubiquitinations Deposited 2016-03-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Mutation：C110A Mutation：C110A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；90mM Tris-HCl (pH 7.8), 3.6% PGA-LM, 25.2% PEG 400, 2-6% Pentaerythritol ethoxylate (3/4 EO/OH)
Resolution 3.33 Å R-free 0.263
5BO0 Crystal structure of Human MCM2 HBD and ASF1b chaperoning a histone H3.2-H4 dimer Deposited 2015-05-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 57–136（80 aa） Fragment：UNP residues 57-136
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；3.2 M sodium formate, 0.1 M Tris, pH 8.5
Resolution 2.91 Å R-free 0.238
5VAC Crystal Structure of ATXR5 SET domain in complex with K36me3 histone H3 peptide Deposited 2017-03-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 19–37（19 aa） Fragment：residues 19-37
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；50% polypropylene glycol 400, 5% DMSO, 0.1 M HEPES-NaOH (pH 6.0)
Resolution 1.95 Å R-free 0.228
6FML CryoEM Structure INO80core Nucleosome complex Deposited 2018-01-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM HEPES pH 8, 60 mM KCl, 0.5% glycerol, 0.25 mM CaCl2, 20 uM ZnCl2, 0.25 mM DTT, 0.05% Octyl-beta-glucoside
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.34 Å
6T79 Structure of a human nucleosome at 3.2 A resolution Deposited 2019-10-21 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 3.20 Å
6T7A Structure of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 3.70 Å
6T7B Structure of human Sox2 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 5.10 Å
6T7C Structure of two copies of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 4.00 Å
6T7D Structure of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 4.40 Å
6X59 The mouse cGAS catalytic domain binding to human assembled nucleosome Deposited 2020-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
6X5A The mouse cGAS catalytic domain binding to human nucleosome that purified from HEK293T cells Deposited 2020-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.36 Å
6XJD Two mouse cGAS catalytic domain binding to human assembled nucleosome Deposited 2020-06-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.80 Å
6Y5D Structure of human cGAS (K394E) bound to the nucleosome Deposited 2020-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain A 39–136（98 aa）
Chain E 39–136（98 aa）
Chain M 39–136（98 aa）
Chain Q 39–136（98 aa）
Not recorded PTD PENTANEDIAL × 9 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6Y5E Structure of human cGAS (K394E) bound to the nucleosome (focused refinement of cGAS-NCP subcomplex) Deposited 2020-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 39–134（96 aa）
Chain E 39–134（96 aa）
Not recorded PTD PENTANEDIAL × 8 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
7BU9 Crystal Structure of Spindlin1-H3(K4me3-K9me2) complex Deposited 2020-04-05 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–16（15 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；3.6M sodium formate, 3% DMSO
Resolution 3.50 Å R-free 0.264
7BU9 Crystal Structure of Spindlin1-H3(K4me3-K9me2) complex Deposited 2020-04-05 Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–16（15 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；3.6M sodium formate, 3% DMSO
Resolution 3.50 Å R-free 0.264
7BU9 Crystal Structure of Spindlin1-H3(K4me3-K9me2) complex Deposited 2020-04-05 Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 2–16（15 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；3.6M sodium formate, 3% DMSO
Resolution 3.50 Å R-free 0.264
7BU9 Crystal Structure of Spindlin1-H3(K4me3-K9me2) complex Deposited 2020-04-05 Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 2–16（15 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；3.6M sodium formate, 3% DMSO
Resolution 3.50 Å R-free 0.264
7JO9 1:1 cGAS-nucleosome complex Deposited 2020-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7JOA 2:1 cGAS-nucleosome complex Deposited 2020-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7JZV Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome Deposited 2020-09-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain P 2–136（135 aa）
Chain p 2–136（135 aa）
Mutation：C110A Mutation：C110A ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7PET The 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 34 PDB declaration: 36-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Chain k 1–136（136 aa）
Chain o 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.50 Å
7PEU Trinucleosome of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
7PEV Nucleosome stack of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.00 Å
7PEW Nucleosome 1 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
7PEX Nucleosome 2 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
7PEY Nucleosome 3 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7PEZ Nucleosome 4 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain k 1–136（136 aa）
Chain o 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.90 Å
7PF0 Trinucleosome of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.00 Å
7PF2 Nucleosome stack of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
7PF3 Nucleosome 4 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain k 1–136（136 aa）
Chain o 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7PF4 Nucleosome 3 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7PF5 Nucleosome 2 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7PF6 Nucleosome 1 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7PFA Trinucleosome of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.70 Å
7PFC Nucleosome stack of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
7PFD Nucleosome 1 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7PFE Nucleosome 2 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7PFF Nucleosome 3 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7PFT Trinucleosome of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.80 Å
7PFU Nucleosome stack of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.00 Å
7PFV Nucleosome 1 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7PFW Nucleosome 2 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.20 Å
7PFX Nucleosome 3 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7TAN Structure of VRK1 C-terminal tail bound to nucleosome core particle Deposited 2021-12-21 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.00 Å
7U50 APE1 bound to a nucleosome core particle with AP-site at SHL-6 Deposited 2022-03-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7U51 Nucleosome core particle with AP-site at SHL-6 Deposited 2022-03-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7U52 nucleosome core particle with AP-site at SHL-6.5 Deposited 2022-03-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7U53 Nucleosome core particle with AP-site at SHL0 Deposited 2022-03-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7UV9 KDM2A-nucleosome structure stabilized by H3K36C-UNC8015 covalent conjugate Deposited 2022-04-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Mutation：K36C Mutation：K36C OH0 N-heptanoyl-N-hydroxy-beta-alanine × 1 FE FE (III) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.20 Å
7UVA Crystal structure of KDM2A histone demethylase catalytic domain in complex with an H3C36 peptide modified by UNC8015 Deposited 2022-04-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 30–42（13 aa） Fragment：UNP residues 30-42
Mutation：K36C FE FE (III) ION × 1 OH0 N-heptanoyl-N-hydroxy-beta-alanine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；100 mM Tris-Cl, pH 8.5, 150 mM lithium sulfate, 20% PEG3350
Resolution 1.98 Å R-free 0.237
7UVA Crystal structure of KDM2A histone demethylase catalytic domain in complex with an H3C36 peptide modified by UNC8015 Deposited 2022-04-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 30–42（13 aa） Fragment：UNP residues 30-42
Mutation：K36C FE FE (III) ION × 1 OH0 N-heptanoyl-N-hydroxy-beta-alanine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；100 mM Tris-Cl, pH 8.5, 150 mM lithium sulfate, 20% PEG3350
Resolution 1.98 Å R-free 0.237
8ATF Nucleosome-bound Ino80 ATPase Deposited 2022-08-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.45 Å
8AV6 CryoEM structure of INO80 core nucleosome complex in closed grappler conformation Deposited 2022-08-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.68 Å
8JLB Cryo-EM structure of the 145 bp human nucleosome containing H3.2 C110A mutant Deposited 2023-06-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Mutation：C110A Mutation：C110A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.36 Å
8JLD Cryo-EM structure of the 145 bp human nucleosome containing acetylated H3 tail Deposited 2023-06-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Mutation：C110A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C110A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.48 Å
8OL1 cGAS-Nucleosome in complex with SPSB3-ELOBC (composite structure) Deposited 2023-03-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 38–135（98 aa）
Chain E 38–135（98 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；PBS buffer
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8VMJ H3K4me3 nucleosome bound to PRC2_AJ119-450 Deposited 2024-01-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain I 1–136（136 aa）
Chain O 1–136（136 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8VMN H3K4me3 nucleosome bound to PRC2_AJ1-450 Deposited 2024-01-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain I 1–136（136 aa）
Chain O 1–136（136 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8VO0 H3K36me3-modified nucleosome bound to PRC2_AJ1-450 with histone H3 tail disengaged Deposited 2024-01-14 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain I 42–136（95 aa）
Chain O 42–136（95 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8VOB H3K36me3-modified nucleosome bound to PRC2_AJ1-450 Deposited 2024-01-14 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain I 1–136（136 aa）
Chain O 1–136（136 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8VWS Nucleosome containing 8oxoG at SHL-6 Deposited 2024-02-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；50 mM HEPES (pH-7.1), 100 mM NaCl, 1 mM TCEP, and 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8VWT OGG1 bound to a nucleosome containing 8oxoG at SHL-6 (composite map) Deposited 2024-02-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；50 mM HEPES (pH-7.1), 100 mM NaCl, 1 mM TCEP, and 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8VWU Nucleosome containing 8oxoG at SHL4 Deposited 2024-02-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；50 mM HEPES (pH-7.1), 100 mM NaCl, 1 mM TCEP, and 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8VWV OGG1 bound to a nucleosome containing 8oxoG at SHL4 (composite map) Deposited 2024-02-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；50 mM HEPES (pH-7.1), 100 mM NaCl, 1 mM TCEP, and 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8X7I Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by intein-based E2-Ub-NCP conjugation strategy Deposited 2023-11-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 38–135（98 aa）
Chain E 38–135（98 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
8X7J Cryo-EM structures of RNF168/UbcH5c-Ub/nucleosomes complex determined by activity-based chemical trapping strategy Deposited 2023-11-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 39–135（97 aa）
Chain E 39–135（97 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
8X7K Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination) Deposited 2023-11-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 39–135（97 aa）
Chain E 39–135（97 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
8ZJR Structure of nucleosome-bound RFX5 complex Deposited 2024-05-15 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8ZJT Structure of free nucleosome Deposited 2024-05-15 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9BE5 Cryo-EM structure of Human Nucleosome collected by EPU on Glacios at 3.3 Angstrom resolution Deposited 2024-04-14 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 39–135（97 aa）
Chain E 39–136（98 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9BE6 Cryo-EM structure of Human Nucleosome collected by Leginon on Krios at 3.0 Angstrom resolution Deposited 2024-04-14 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 39–135（97 aa）
Chain E 40–136（97 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9D3K Two Dsup molecules in complex with the nucleosome open from both sides Deposited 2024-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 42–136（95 aa）
Chain E 42–136（95 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
9D3L Two Dsup molecules in complex with the nucleosome open from the left side Deposited 2024-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 39–136（98 aa）
Chain E 39–136（98 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9D3M Two HMGN2s in complex with the nucleosome Deposited 2024-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 38–136（99 aa）
Chain E 38–136（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9D3N 167-bp 5S rDNA nucleosome cross-linked with glutaraldehyde Deposited 2024-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 45–134（90 aa）
Chain E 45–134（90 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9D3O 167-bp 5S rDNA nucleosome - closed Deposited 2024-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 38–136（99 aa）
Chain E 38–136（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9D3P 167-bp 5S rDNA nucleosome - open I (open only on the downstream side) Deposited 2024-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 38–136（99 aa）
Chain E 38–136（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
9D3Q 167-bp 5S rDNA nucleosome - open II Deposited 2024-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 41–136（96 aa）
Chain E 41–136（96 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9D3R 147-bp 5S rDNA nucleosome - closed Deposited 2024-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 40–136（97 aa）
Chain E 40–136（97 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9D3S 147-bp 5S rDNA nucleosome - open I (open on the downstream side) Deposited 2024-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 38–136（99 aa）
Chain E 38–136（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9D3T 147-bp 5S rDNA nucleosome cross-linked with glutaraldehyde Deposited 2024-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 44–136（93 aa）
Chain E 44–136（93 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9DWF Nucleosome containing a 1-nt gap at SHL-4.5 Deposited 2024-10-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9DWG DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 1, composite) Deposited 2024-10-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9DWH DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 2, composite) Deposited 2024-10-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9DWI DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 3, composite) Deposited 2024-10-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9DWJ Nucleosome containing a 1-nt gap at SHL-3.5 Deposited 2024-10-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9DWK DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-3.5 Deposited 2024-10-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: dodecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
9DWL Nucleosome containing a 1-nt gap at SHL-5.5 Deposited 2024-10-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
9DWM DNA polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-5.5 Deposited 2024-10-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: dodecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9E00 Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Deposited 2024-10-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Not recorded ZN ZINC ION × 9 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.75 Å
9E05 The consensus model of the cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Deposited 2024-10-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.00 Å
9E09 Cryo-EM structure a single nucleosome (2) focus of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Deposited 2024-10-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.72 Å
9E0R Cryo-EM structure of a single nucleosome (1) focus of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Deposited 2024-10-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9E2D Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to a di-nucleosome with a five base pair linker Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.08 Å
9E2F Cryo-EM structure of a di-nucleosome with a five base pair linker Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.90 Å
9E2Q Cryo-EM structure of DNMT 3A2/3B3 tetramer in complex with a di-nucleosome with a six base pair linker Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.14 Å
9E2R Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to a di-nucleosome and an histone-3 peptide Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.71 Å
9E3D Cryo-EM structure of DNMT 3A2/3B3 tetramer in complex with a di-nucleosome with K120R mutant H2B Deposited 2024-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Not recorded ZN ZINC ION × 9 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9E3R Cryo-EM structure of PWWP domain deleted DNMT 3A2/3B3 in complex with a di-nucleosome Deposited 2024-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
9E3U Cryo-EM structure of DNMT 3A2/3B3 tetramer bound to a di-nucleosome with a 25 base-pair linker Deposited 2024-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded ZN ZINC ION × 9 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.90 Å
9E49 Cryo-EM structure of a di-nucleosome with an eight base-pair linker Deposited 2024-10-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.93 Å
9GMK SIRT7:H3K18DTU nucleosome complex Deposited 2024-08-29 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9GMR SIRT7-H3K36MTUnucleosome complex Deposited 2024-08-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded A1IY0 [[(2~{R},3~{a}~{R},5~{R},6~{R},6~{a}~{R})-2-(methylamino)-6-oxidanyl-2-(propylamino)-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxathiol-5-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9GW2 State 2 MAP 1 SETD2 bound to proximal H3 of upstream nucleosome Deposited 2024-09-26 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.84 Å
9IPU cryo-EM structure of the RNF168(1-193)/UbcH5c-Ub ubiquitylation module bound to H1.0-K63-Ub3 modified chromatosome Deposited 2024-07-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
9NQU KDM6B-nucleosome structure stabilized by H3K27C-UNC8015 covalent conjugate Deposited 2025-03-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded FE FE (III) ION × 1 ZN ZINC ION × 1 OH0 N-heptanoyl-N-hydroxy-beta-alanine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.16 Å
9OGR Cryo-EM analysis of human H2A.Z on methylated Sat2R-P DNA (v1) Deposited 2025-05-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.78 Å
9OGS Cryo-EM analysis of human H2A.Z on Sat2R-P DNA (v1) Deposited 2025-05-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
9OGZ Cryo-EM analysis of human H2A.Z on Sat2R-P DNA (v2) Deposited 2025-05-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
9OH0 Cryo-EM analysis of human H2A.Z on methylated Sat2R-P DNA (v2) Deposited 2025-05-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.78 Å
9OH1 Cryo-EM analysis of human H2A.Z on 601L DNA Deposited 2025-05-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
9OH2 Cryo-EM analysis of human H2A.Z on methylated 601L DNA Deposited 2025-05-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.14 Å
9RZC State 3 MAP 1 SETD2 bound to distal H3 of upstream nucleosome Deposited 2025-07-15 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.66 Å
9RZE State 2 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to proximal upstream H3 Deposited 2025-07-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.53 Å
9S0U State 3 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to distal upstream H3 Deposited 2025-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.72 Å
9S3G State 1 MAP3 RNA Pol II activated elongation complex with SETD2 and upstream hexasome Deposited 2025-07-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
9U5U The 1:1 cryo-EM structure of BAP1/ASXL1-K351Ub in complex with H2AK119Ub nucleosome Deposited 2025-03-21 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
9Y46 Human nucleosome structure on Nickel-NTA lipid affinity grid (C2 refinement) Deposited 2025-09-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.59 Å
9Y47 Human nucleosome structure on Nickel-NTA lipid affinity grid (C1 refinement) Deposited 2025-09-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.74 Å
9ZEN Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1B2 Deposited 2025-11-30 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain A 39–135（97 aa）
Chain E 39–135（97 aa）
Mutation：C97S Mutation：C97S No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES pH7.6, 50 mM NaCl, 0.5 mM MgCl2, 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.17 Å

139 other PDB entries and 154 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H32_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–15； UniProt 2–16 Author chain D； PDBConstruct 1–15； UniProt 2–16 Author chain F； PDBConstruct 1–15； UniProt 2–16 Author chain H； PDBConstruct 1–15； UniProt 2–16

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 7bqz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7bqz
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7bqz
Deposition date deposition_date2020-03-26
Structure title titleCrystal Structure of Spindlin1 bound to H3(K4me3-K9me3) peptide
Keywords keywordsSpin/Ssty repeat, GENE REGULATION; GENE REGULATION
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier35.15 Å
Radius of gyration Rg (electron density) rg_electron34.11 Å
Forward intensity I(0) i0156137000.00
Molecular weight molecular_weight100320.0 kDa
Excluded volume excluded_volume125720 ų
Envelope volume envelope_volume178340 ų
Hydration-shell volume shell_volume43224 ų
Envelope diameter envelope_diameter120.1 Å
Shell Rg shell_rg41.38 Å
Envelope Rg envelope_rg33.23 Å
Shape Rg shape_rg34.13 Å
Total Rg total_rg34.60 Å
Total atoms total_atoms7064
Residues n_residues867
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 dmax118.3 Å
Rg (real space) rg_real35.03 Å
Rg uncertainty (real space) rg_real_error1.08 Å
I(0) (real space) i0_real1.5610e+08
I(0) uncertainty (real space) i0_real_error2.5990e+06
Rg (reciprocal space) rg_reciprocal35.10 Å
I(0) (reciprocal space) i0_reciprocal156100000.0000
Solution quality estimate total_estimate0.8933
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary47.3 Å
Skewness Skewness skewness0.145
Kurtosis Kurtosis kurtosis-0.582
Angular range angular_range— – 0.2250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha35830000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.872; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.997
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)