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4tmp

Crystal structure of AF9 YEATS bound to H3K9ac peptide

Method: X-RAY DIFFRACTION Dmax: 107.9 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein AF-9

Homo sapiens

UniProt P42568

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 1–138 Fragment：YEATS domain (UNP residues 1-138) ALA-ARG-THR-LYS-GLN-THR-ALA-ARG-ALY-SER-THR × 1 （P84243） EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；291 K；20% PEG4000, 5% 2-Propanol, 0.1 M Sodium Citrate Tribasic Dihydrate Resolution 2.30 Å R-free 0.229
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 1–138 Fragment：YEATS domain (UNP residues 1-138) ALA-ARG-THR-LYS-GLN-THR-ALA-ARG-ALY-SER-THR × 1 （P84243） EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；291 K；20% PEG4000, 5% 2-Propanol, 0.1 M Sodium Citrate Tribasic Dihydrate Resolution 2.30 Å R-free 0.229

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 4TMP Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2LM0 Solution structure of the AF4-AF9 complex Deposited 2011-11-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 490–568（79 aa） Fragment：UNP residues 738-779, UNP residues 490-568
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient
NMR sample composition 9.3 mM Bis-Tris, 15.8 mM MES, 100 mM sodium chloride, 1 mM DTT, 5 % D-99% D2O, 400 uM [U-100% 13C; U-100% 15N] Protein, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 15.8 mM MES, 9.3 mM Bis-Tris, 100 mM sodium chloride, 1 mM DTT, 5 % D-99% D2O, 2 mM [U-100% 13C; U-100% 15N] protein, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 9.3 mM Bis-Tris, 15.8 mM MES, 100 mM sodium chloride, 1 mM DTT, 5 % D-99% D2O, 400 uM [U-100% 13C; U-100% 15N] Protein, 3.5 % (3-acrylamidopropyl)-trimethylammonium chloride, 3.5 % acrylic acid, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 9.3 mM Bis-Tris, 15.8 mM MES, 100 mM sodium chloride, 1 mM DTT, 5 % D-99% D2O, 400 uM [U-100% 13C; U-100% 15N] Protein, 3.5 % (3-acrylamidopropyl)-trimethylammonium chloride, 3.5 % acrylamide, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
2MV7 Solution NMR structure of DOT1L in complex with AF9 (DOT1L-AF9) Deposited 2014-09-24 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 500–568（69 aa） Fragment：UNP RESIDUES 500-568
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 100；Pressure AMBIENT
NMR sample composition 750 uM [U-100% 13C; U-100% 15N] PROTEIN AF, 750 uM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC, 9.3 mM BIS-TRIS, 15.8 mM MES, 100 mM SODIUM CHLORIDE, 1 mM DTT, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 750 mM [U-100% 13C; U-100% 15N] PROTEIN AF, 750 mM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC, 9.3 mM BIS-TRIS, 15.8 mM MES, 100 mM SODIUM CHLORIDE, 1 mM DTT, 3.5 % (3-ACRYLAMIDOPROPYL)-TRIMETHYLAMMONIUM CHLORIDE, 3.5 % ACRYLIC ACID, 750 mM [U-100% 13C; U-100% 15N] PROTEIN AF, 750 mM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC, 9.3 mM BIS-TRIS, 15.8 mM MES, 100 mM SODIUM CHLORIDE, 1 mM DTT, 3.5 % (3-ACRYLAMIDOPROPYL)-TRIMETHYLAMMONIUM CHLORIDE, 3.5 % ACRYLAMIDE, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 750 mM [U-100% 13C; U-100% 15N] PROTEIN AF, 750 mM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC, 9.3 mM BIS-TRIS, 15.8 mM MES, 100 mM SODIUM CHLORIDE, 1 mM DTT, 3.5 % (3-ACRYLAMIDOPROPYL)-TRIMETHYLAMMONIUM CHLORIDE, 3.5 % ACRYLIC ACID, 750 mM [U-100% 13C; U-100% 15N] PROTEIN AF, 750 mM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC, 9.3 mM BIS-TRIS, 15.8 mM MES, 100 mM SODIUM CHLORIDE, 1 mM DTT, 3.5 % (3-ACRYLAMIDOPROPYL)-TRIMETHYLAMMONIUM CHLORIDE, 3.5 % ACRYLAMIDE, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
2N4Q Solution NMR structure of CBX8 in complex with AF9 (CBX8-AF9) Deposited 2015-06-30 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 500–568（69 aa） Fragment：UNP residues 500-568
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient
NMR sample composition 750 uM [U-100% 13C; U-100% 15N] Chromobox protein homolog 8, 750 uM [U-100% 13C; U-100% 15N] Protein AF, 9.5 mM BIS-TRIS, 15.8 mM MES, 100 mM sodium chloride, 1 mM DTT, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
2NDF Solution NMR structures of AF9 yeats domain in complex with histon H3 acetylation at K18 Deposited 2016-05-19 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–138（138 aa） Fragment：YEATS domain residues 1-138
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Pressure ambient
NMR sample composition 10 mM sodium phosphate, 500 mM sodium chloride, 2 mM EDTA, 2 mM [U-100% 2H] DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 10 mM sodium phosphate, 500 mM sodium chloride, 2 mM EDTA, 2 mM [U-100% 2H] DTT, 100% D2O | 100% D2O
Resolution not provided
2NDG Solution NMR structures of AF9 yeats domain in complex with histone H3 crotonylation at K18 Deposited 2016-05-19 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–138（138 aa） Fragment：YEATS domain residues 1-138
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Pressure ambient
NMR sample composition 10 mM sodium phosphate, 500 mM sodium chloride, 2 mM EDTA, 2 mM [U-100% 2H] DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 10 mM sodium phosphate, 500 mM sodium chloride, 2 mM EDTA, 2 mM [U-100% 2H] DTT, 100% D2O | 100% D2O
Resolution not provided
5HJB AF9 YEATS in complex with histone H3 Crotonylation at K9 Deposited 2016-01-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–138（138 aa） Fragment：YEATS domain, UNP residues 1-138
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；20% (w/v) polyethylene glycol 4000, 0.2 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, 3% MPD
Resolution 2.70 Å R-free 0.253
5HJD AF9 YEATS in complex with histone H3 Crotonylation at K18 Deposited 2016-01-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–138（138 aa） Fragment：YEATS domain, UNP residues 1-138
Chain C 1–138（138 aa） Fragment：YEATS domain, UNP residues 1-138
Chain E 1–138（138 aa） Fragment：YEATS domain, UNP residues 1-138
Chain G 1–138（138 aa） Fragment：YEATS domain, UNP residues 1-138
Not recorded CU COPPER (II) ION × 3 SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；20%(w/v) polyethylene glycol 4000, 0.2 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, 0.1 M copper chloride dihydrate
Resolution 2.81 Å R-free 0.273
5HJD AF9 YEATS in complex with histone H3 Crotonylation at K18 Deposited 2016-01-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain K 1–138（138 aa） Fragment：YEATS domain, UNP residues 1-138
Chain N 1–138（138 aa） Fragment：YEATS domain, UNP residues 1-138
Chain Q 1–138（138 aa） Fragment：YEATS domain, UNP residues 1-138
Chain T 1–138（138 aa） Fragment：YEATS domain, UNP residues 1-138
Not recorded CU COPPER (II) ION × 1 SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；20%(w/v) polyethylene glycol 4000, 0.2 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, 0.1 M copper chloride dihydrate
Resolution 2.81 Å R-free 0.273
5YYF Crystal structure of AF9 YEATS domain in complex with a peptide inhibitor "PHQ-H3(Q5-K9)" modified at K9 with 2-furancarboyl group Deposited 2017-12-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–138（138 aa）
Not recorded SO4 SULFATE ION × 2 FOA 2-FUROIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.2M ammonium sulfate, 0.1M sodium citrate tribasic dihydrate, pH 5.6, 25 % (w/v) PEG 4000
Resolution 1.90 Å R-free 0.224
5YYF Crystal structure of AF9 YEATS domain in complex with a peptide inhibitor "PHQ-H3(Q5-K9)" modified at K9 with 2-furancarboyl group Deposited 2017-12-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–138（138 aa）
Not recorded SO4 SULFATE ION × 1 FOA 2-FUROIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.2M ammonium sulfate, 0.1M sodium citrate tribasic dihydrate, pH 5.6, 25 % (w/v) PEG 4000
Resolution 1.90 Å R-free 0.224
6B7G Solution NMR structure of BCoR in complex with AF9 (BCoR-AF9) Deposited 2017-10-04 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 497–565（69 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient
NMR sample composition 750 uM [U-13C; U-15N] BCoR, 750 uM [U-13C; U-15N] AF9, 9.3 mM Bis-Tris, 15.8 mM MES, 100 mM NaCl, 1 mM DTT, 5 % [U-99% 2H] D2O, 95 % H2O, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
6L5Z Crystal strucutre of AF9 YEATS domain in complex with a cyclopeptide inhibitor Deposited 2019-10-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–138（138 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20% (w/v)PEG 3350,0.2M Ammonium Nitrate
Resolution 3.05 Å R-free 0.222
6LS6 Crystal Structure of YEATS domain of AF9 in complex with H3K9bz peptide Deposited 2020-01-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–138（138 aa） Fragment：YEATS domain of AF9
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；0.1 M Bis-Tris, pH 5.5??200 mM lithium sulfate, 25% w/v PEG 3350.
Resolution 2.20 Å R-free 0.272
6LS6 Crystal Structure of YEATS domain of AF9 in complex with H3K9bz peptide Deposited 2020-01-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–138（138 aa） Fragment：YEATS domain of AF9
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；0.1 M Bis-Tris, pH 5.5??200 mM lithium sulfate, 25% w/v PEG 3350.
Resolution 2.20 Å R-free 0.272
6MIL Crystal structure of AF9 YEATS domain in complex with histone H3K9bu Deposited 2018-09-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–138（138 aa） Fragment：YEATS domain residues 1-138
Not recorded PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；200 mM sodium malonate, 100 mM Bis-Tris propane pH 8.5, and 20% (w/v) PEG 3350
Resolution 1.93 Å R-free 0.236
6MIL Crystal structure of AF9 YEATS domain in complex with histone H3K9bu Deposited 2018-09-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–138（138 aa） Fragment：YEATS domain residues 1-138
Not recorded MLI MALONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；200 mM sodium malonate, 100 mM Bis-Tris propane pH 8.5, and 20% (w/v) PEG 3350
Resolution 1.93 Å R-free 0.236
6MIM Crystal structure of AF9 YEATS domain Y78W mutant in complex with histone H3K9cr Deposited 2018-09-19 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 A 1–138（138 aa） Fragment：YEATS domain residues 1-138
Mutation：Y78W No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；100 mM MES pH 6.0, 20%(w/v) PEG 6000, and 10 mM ZnCl2
Resolution 2.52 Å R-free 0.264
6MIM Crystal structure of AF9 YEATS domain Y78W mutant in complex with histone H3K9cr Deposited 2018-09-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–138（138 aa） Fragment：YEATS domain residues 1-138
Mutation：Y78W No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；100 mM MES pH 6.0, 20%(w/v) PEG 6000, and 10 mM ZnCl2
Resolution 2.52 Å R-free 0.264
7EIC Crystal structure of AF9 YEATS domain in complex with H4K5acK8ac peptide Deposited 2021-03-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–138（138 aa）
Not recorded GOL GLYCEROL × 2 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Bis-Tris buffer (pH 6.5) containing 100 mM ammonium acetate and 25% PEG3350
Resolution 1.95 Å R-free 0.205
7EIC Crystal structure of AF9 YEATS domain in complex with H4K5acK8ac peptide Deposited 2021-03-30 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 1–138（138 aa）
Not recorded GOL GLYCEROL × 2 PEG DI(HYDROXYETHYL)ETHER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Bis-Tris buffer (pH 6.5) containing 100 mM ammonium acetate and 25% PEG3350
Resolution 1.95 Å R-free 0.205
7EID Crystal structure of AF9 YEATS domain in complex with H4K8acK12ac peptide Deposited 2021-03-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–138（138 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；200 mM ammonium citrate tribasic buffer (pH 7.0) containing 19% PEG3350
Resolution 2.00 Å R-free 0.229
7EID Crystal structure of AF9 YEATS domain in complex with H4K8acK12ac peptide Deposited 2021-03-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–138（138 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；200 mM ammonium citrate tribasic buffer (pH 7.0) containing 19% PEG3350
Resolution 2.00 Å R-free 0.229
7VKG Crystal structure of AF9 YEATS domain in complex with Compound 10 Deposited 2021-09-29 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 1–138（138 aa）
Not recorded 7IV ~{N}-(4-chlorophenyl)-2-phenylmethoxy-ethanamide × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M trimethylamine N-oxide dehydrate, 0.1 M Tris, 20% w/v PEGMME 2000, pH 8.5
Resolution 1.83 Å R-free 0.245
7VKH Crystal structure of AF9 YEATS domain in complex with hit 2 Deposited 2021-09-30 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 1–138（138 aa）
Not recorded 7IY ~{N}-(3-azanyl-4-chloranyl-phenyl)-2-methoxy-ethanamide × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M trimethylamine N-oxide dehydrate, 0.1 M Tris, 20% w/v PEGMME 2000, pH 8.5
Resolution 2.25 Å R-free 0.244
7VKH Crystal structure of AF9 YEATS domain in complex with hit 2 Deposited 2021-09-30 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 1–138（138 aa）
Not recorded 7IY ~{N}-(3-azanyl-4-chloranyl-phenyl)-2-methoxy-ethanamide × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M trimethylamine N-oxide dehydrate, 0.1 M Tris, 20% w/v PEGMME 2000, pH 8.5
Resolution 2.25 Å R-free 0.244
8PJ7 MLLT3 in complex with compound PFI-6 Deposited 2023-06-22 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 1–142（142 aa）
Not recorded ZJ9 ~{N}-[(1~{R})-2,3-dihydro-1~{H}-inden-1-yl]-5-[4-(dimethylcarbamoyl)-3-oxidanyl-phenyl]-1,2-oxazole-3-carboxamide × 1 EDO 1,2-ETHANEDIOL × 6 DMS DIMETHYL SULFOXIDE × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Bis-Tris pH=7.0 150 mM AmSO4 Gradient 20-30% PEG3350
Resolution 1.26 Å R-free 0.222
8TLW Crystal structure of MBP and AF9 AHD fusion protein 3AQA in complex with peptidomimetic inhibitor 28 Deposited 2023-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 500–568（69 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20-30% PEG3350, 0.1 M Bis-Tris pH 5.5
Resolution 2.11 Å R-free 0.213
8TLX Crystal structure of MBP and AF9 AHD fusion protein 3AQA in complex with peptidomimetic inhibitor 21a Deposited 2023-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 500–568（69 aa）
Not recorded GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20-30% PEG3350 and 0.1 M Bis-Tris pH 5.5
Resolution 2.10 Å R-free 0.227
8Z73 Crystal Structure of AF9 in complex with H3K9la peptide Deposited 2024-04-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–138（138 aa） Fragment：N-terminally processed
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2.4M Sodium Malonate
Resolution 2.91 Å R-free 0.221
8Z73 Crystal Structure of AF9 in complex with H3K9la peptide Deposited 2024-04-19 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–138（138 aa） Fragment：N-terminally processed
Not recorded EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2.4M Sodium Malonate
Resolution 2.91 Å R-free 0.221
8Z73 Crystal Structure of AF9 in complex with H3K9la peptide Deposited 2024-04-19 Different construct Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–138（138 aa） Fragment：N-terminally processed
Not recorded EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2.4M Sodium Malonate
Resolution 2.91 Å R-free 0.221
8Z73 Crystal Structure of AF9 in complex with H3K9la peptide Deposited 2024-04-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–138（138 aa） Fragment：N-terminally processed
Not recorded EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2.4M Sodium Malonate
Resolution 2.91 Å R-free 0.221
9ARO Crystal structure of AF9 YEATS domain in complex with acetylated at K1007 MOZ Deposited 2024-02-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–138（138 aa） Fragment：YEATS domain
Chain B 1–138（138 aa） Fragment：YEATS domain
Not recorded FMT FORMIC ACID × 2 PEG DI(HYDROXYETHYL)ETHER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；291 K；0.2 M Sodium formate pH 7.2, 20% (w/v) PEG 3350
Resolution 2.30 Å R-free 0.273
9ARO Crystal structure of AF9 YEATS domain in complex with acetylated at K1007 MOZ Deposited 2024-02-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–138（138 aa） Fragment：YEATS domain
Chain D 1–138（138 aa） Fragment：YEATS domain
Not recorded FMT FORMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；291 K；0.2 M Sodium formate pH 7.2, 20% (w/v) PEG 3350
Resolution 2.30 Å R-free 0.273
9ARR Crystal structure of AF9 YEATS domain in complex with dicrotonylated at K1007 and K1014 MOZ Deposited 2024-02-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–138（138 aa） Fragment：YEATS domain
Chain B 1–138（138 aa） Fragment：YEATS domain
Not recorded LI LITHIUM ION × 2 NO3 NITRATE ION × 4 PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；291 K；0.2 M Lithium nitrate pH 7.1, 20% w/v PEG 3350
Resolution 2.10 Å R-free 0.247
9IM4 Crystal Structure of AF9 YEATS domain F28R mutant in complex with histone H3K9la Deposited 2024-07-02 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 A 1–138（138 aa）
Mutation：F28R No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2.1M DL Malic acid pH7.0
Resolution 2.79 Å R-free 0.315
9IM4 Crystal Structure of AF9 YEATS domain F28R mutant in complex with histone H3K9la Deposited 2024-07-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–138（138 aa）
Mutation：F28R No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2.1M DL Malic acid pH7.0
Resolution 2.79 Å R-free 0.315

24 other PDB entries and 37 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AF9_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–141； UniProt 1–138 Author chain C； PDBConstruct 4–141； UniProt 1–138

ALA-ARG-THR-LYS-GLN-THR-ALA-ARG-ALY-SER-THR

OrganismNot specified

UniProt P84243

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 2–12 Fragment：UNP residues 2-12 Non-standard monomer：Yes (specific site not provided by mmCIF) Protein AF-9 × 1 （P42568） EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；291 K；20% PEG4000, 5% 2-Propanol, 0.1 M Sodium Citrate Tribasic Dihydrate Resolution 2.30 Å R-free 0.229
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 2–12 Fragment：UNP residues 2-12 Non-standard monomer：Yes (specific site not provided by mmCIF) Protein AF-9 × 1 （P42568） EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；291 K；20% PEG4000, 5% 2-Propanol, 0.1 M Sodium Citrate Tribasic Dihydrate Resolution 2.30 Å R-free 0.229

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 4TMP Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2L43 Structural basis for histone code recognition by BRPF2-PHD1 finger Deposited 2010-10-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–13（12 aa）
Mutation：C29S, C36S ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 6.7；293 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient
NMR sample composition 0.8mM [U-100% 13C; U-100% 15N] protein-1, 1.6mM ZINC ION-2, 20mM Bis-Tris-3, 150mM sodium chloride-4, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.8mM [U-100% 13C; U-100% 15N] protein-5, 1.6mM ZINC ION-6, 20mM Bis-Tris-7, 150mM sodium chloride-8, 100% D2O | 100% D2O
Resolution not provided
3ASK Structure of UHRF1 in complex with histone tail Deposited 2010-12-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 2–14（13 aa） Fragment：residues in UNP 2-14
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M Bis-Tris propane, 200mM sodium citrate, 20% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.90 Å R-free 0.286
3ASK Structure of UHRF1 in complex with histone tail Deposited 2010-12-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain Q 2–14（13 aa） Fragment：residues in UNP 2-14
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M Bis-Tris propane, 200mM sodium citrate, 20% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.90 Å R-free 0.286
3ASK Structure of UHRF1 in complex with histone tail Deposited 2010-12-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain R 2–14（13 aa） Fragment：residues in UNP 2-14
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M Bis-Tris propane, 200mM sodium citrate, 20% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.90 Å R-free 0.286
3ASL Structure of UHRF1 in complex with histone tail Deposited 2010-12-16 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 2–12（11 aa） Fragment：residues in UNP 2-12
Not recorded ZN ZINC ION × 4 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；10mM sodium citrate, 42% PEGMME2000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.41 Å R-free 0.196
3AV2 The human nucleosome structure containing the histone variant H3.3 Deposited 2011-02-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.272
3JVK Crystal structure of bromodomain 1 of mouse Brd4 in complex with histone H3-K(ac)14 Deposited 2009-09-17 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 13–20（8 aa） Fragment：UNP residues 13-20
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；3.6M Na formate, 10% glycerol, soaked with 10-times excess of histone peptide, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.80 Å R-free 0.259
3MUK Crystal structure of Brd4 bromodomain 1 with propionylated histone H3-K(prop)23 Deposited 2010-05-03 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 22–29（8 aa） Fragment：histone H3 peptide, UNP residues 22-29
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；3.6M Na formate, 10% glycerol, soaked with 20-times excess of histone octapeptide, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.75 Å R-free 0.219
3MUL Crystal structure of Brd4 bromodomain 1 with butyrylated histone H3-K(buty)14 Deposited 2010-05-03 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 13–20（8 aa） Fragment：histone H3 peptide, UNP residues 13-20
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；3.6M Na formate, 10% glycerol, soaked with 20-times excess of histone octapeptide, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.65 Å R-free 0.226
3QL9 Monoclinic complex structure of ATRX ADD bound to histone H3K9me3 peptide Deposited 2011-02-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–16（15 aa） Fragment：K9 trimethylated H3 N-terminal fragment, UNP residues 2-16
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；277 K；14% PEG 4000, 0.1M MES, 0.2 M KCL, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 0.93 Å R-free 0.131
3QLA Hexagonal complex structure of ATRX ADD bound to H3K9me3 peptide Deposited 2011-02-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–16（15 aa） Fragment：N-terminal tail, UNP residues 2-16
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 3 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；277 K；14% PEG 4000, 0.1M MES, 0.2M KCL, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.60 Å R-free 0.179
3QLA Hexagonal complex structure of ATRX ADD bound to H3K9me3 peptide Deposited 2011-02-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 2–16（15 aa） Fragment：N-terminal tail, UNP residues 2-16
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；277 K；14% PEG 4000, 0.1M MES, 0.2M KCL, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.60 Å R-free 0.179
3QLC Complex structure of ATRX ADD domain bound to unmodified H3 1-15 peptide Deposited 2011-02-02 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 2–16（15 aa） Fragment：N-terminal tail, UNP residues 2-16
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；24% PEG 3350, 0.1M HEPES-NaOH, 0.2M KCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.50 Å R-free 0.241
3QLC Complex structure of ATRX ADD domain bound to unmodified H3 1-15 peptide Deposited 2011-02-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–16（15 aa） Fragment：N-terminal tail, UNP residues 2-16
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；24% PEG 3350, 0.1M HEPES-NaOH, 0.2M KCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.50 Å R-free 0.241
3WTP Crystal Structure of the heterotypic nucleosome containing human CENP-A and H3.3 Deposited 2014-04-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
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 2.67 Å R-free 0.270
4GNE Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3 peptide 1-7 Deposited 2012-08-17 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 2–8（7 aa） Fragment：UNP RESIDUES 2-8
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；283 K；0.1M Tris-HCl pH 7.0, 30% (w/v) PEG 3000, 0.2M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 1.47 Å R-free 0.178
4GNF Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3 peptide 1-15 Deposited 2012-08-17 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 2–16（15 aa） Fragment：UNP RESIDUES 2-16
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；283 K；0.1M Hepes pH 7.5, 70% v/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 1.55 Å R-free 0.205
4GNG Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3K9me3 peptide Deposited 2012-08-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–16（15 aa） Fragment：UNP RESIDUES 2-16
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 4 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；283 K；0.1M Mes pH 6.5, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 1.73 Å R-free 0.214
4GNG Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3K9me3 peptide Deposited 2012-08-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 2–16（15 aa） Fragment：UNP RESIDUES 2-16
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；283 K；0.1M Mes pH 6.5, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 1.73 Å R-free 0.214
4GU0 Crystal structure of LSD2 with H3 Deposited 2012-08-29 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 E 2–27（26 aa） Fragment：UNP residues 2-27
Mutation：K4M FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2M (NH4)2 Tartrate, 0.1M HEPES, 10% PEG20000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.10 Å R-free 0.221
4GU0 Crystal structure of LSD2 with H3 Deposited 2012-08-29 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 2–27（26 aa） Fragment：UNP residues 2-27
Mutation：K4M FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2M (NH4)2 Tartrate, 0.1M HEPES, 10% PEG20000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.10 Å R-free 0.221
4GUR Crystal structure of LSD2-NPAC with H3 in space group P21 Deposited 2012-08-29 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 2–22（21 aa） Fragment：UNP residues 2-22
Mutation：K4M FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 1 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.02M Citric acid, 0.03M Bis_tris propane, 10% PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.51 Å R-free 0.204
4GUS Crystal structure of LSD2-NPAC with H3 in space group P3221 Deposited 2012-08-29 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 2–22（21 aa） Fragment：UNP residues 2-22
Mutation：K4M FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 IOD IODIDE ION × 6 GOL GLYCEROL × 2 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；277 K；0.1M Ammonium Iodide, 0.1M MES, 10% PEG3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.23 Å R-free 0.237
4GY5 Crystal structure of the tandem tudor domain and plant homeodomain of UHRF1 with Histone H3K9me3 Deposited 2012-09-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 2–18（17 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；20% PEG 3350, 200mM Ammonium Tartrate, 100mM Bis-Tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.96 Å R-free 0.288
4GY5 Crystal structure of the tandem tudor domain and plant homeodomain of UHRF1 with Histone H3K9me3 Deposited 2012-09-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 2–18（17 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；20% PEG 3350, 200mM Ammonium Tartrate, 100mM Bis-Tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.96 Å R-free 0.288
4H9N Complex structure 1 of DAXX/H3.3(sub5)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–136（135 aa）
Mutation：S96A, Y99F, G102A, A111T, M120F PO4 PHOSPHATE ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1.8 M Na/K-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.95 Å R-free 0.209
4H9O Complex structure 2 of DAXX/H3.3(sub5,G90M)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–136（135 aa）
Mutation：G90M, S96A, Y99F, G102A, A111T, M120F PO4 PHOSPHATE ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1.8 M Na/K-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.05 Å R-free 0.225
4H9P Complex structure 3 of DAXX/H3.3(sub5,G90A)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–136（135 aa）
Mutation：G90A, S96A, Y99F, G102A, A111T, M120F PO4 PHOSPHATE ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；1.8 M Na/K-phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.20 Å R-free 0.242
4H9P Complex structure 3 of DAXX/H3.3(sub5,G90A)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 2–136（135 aa）
Mutation：G90A, S96A, Y99F, G102A, A111T, M120F PO4 PHOSPHATE ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；1.8 M Na/K-phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.20 Å R-free 0.242
4H9Q Complex structure 4 of DAXX(E225A)/H3.3(sub5)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–136（135 aa）
Mutation：S96A, Y99F, G102A, A111T, M120F PO4 PHOSPHATE ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1.8 M Na/K-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.95 Å R-free 0.221
4H9Q Complex structure 4 of DAXX(E225A)/H3.3(sub5)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 2–136（135 aa）
Mutation：S96A, Y99F, G102A, A111T, M120F PO4 PHOSPHATE ION × 18 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1.8 M Na/K-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.95 Å R-free 0.221
4H9R Complex structure 5 of DAXX(E225A)/H3.3(sub5,G90A)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–136（135 aa）
Mutation：G90A, S96A, Y99F, G102A, A111T, M120F PO4 PHOSPHATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；1.6 M Na/K-phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.20 Å R-free 0.230
4H9R Complex structure 5 of DAXX(E225A)/H3.3(sub5,G90A)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 2–136（135 aa）
Mutation：G90A, S96A, Y99F, G102A, A111T, M120F PO4 PHOSPHATE ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；1.6 M Na/K-phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.20 Å R-free 0.230
4H9S Complex structure 6 of DAXX/H3.3(sub7)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–136（135 aa）
Mutation：A75C, F84W, S96A, Y99F, G102A, A111T, M120F PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；0.1 M Na/K-phosphate, 2.5M NaCl, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.250
4H9S Complex structure 6 of DAXX/H3.3(sub7)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–136（135 aa）
Mutation：A75C, F84W, S96A, Y99F, G102A, A111T, M120F PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；0.1 M Na/K-phosphate, 2.5M NaCl, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.250
4H9S Complex structure 6 of DAXX/H3.3(sub7)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 2–136（135 aa）
Chain B 2–136（135 aa）
Mutation：A75C, F84W, S96A, Y99F, G102A, A111T, M120F Mutation：A75C, F84W, S96A, Y99F, G102A, A111T, M120F PO4 PHOSPHATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；0.1 M Na/K-phosphate, 2.5M NaCl, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.250
4HGA Structure of the variant histone H3.3-H4 heterodimer in complex with its chaperone DAXX Deposited 2012-10-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–136（136 aa）
Not recorded PC4 TETRACHLOROPLATINATE(II) × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；298 K；0.1M HEPES-Na, pH 7.6, 23% (v/v) PEG 3350, 0.25M Ammonium acetate, 1% Tacsimate pH 7.0, 6% ethanol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.80 Å R-free 0.271
4N4I Crystal structure of the Bromo-PWWP of the mouse zinc finger MYND-type containing 11 isoform alpha in complex with histone H3.3K36me3 Deposited 2013-10-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 20–43（24 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；289 K；25% (w/v) polyethylene glycol 4000, 0.1M Tris-HCl, pH 8.3, 0.2M Li2SO4, vapor diffusion, hanging drop, temperature 289K
Resolution 2.00 Å R-free 0.245
4QQ4 CW-type zinc finger of MORC3 in complex with the amino terminus of histone H3 Deposited 2014-06-26 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 C 2–16（15 aa） Fragment：unp residues 2-16
Chain D 2–16（15 aa） Fragment：unp residues 2-16
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 3 UNX UNKNOWN LIGAND × 7 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG-3350, 0.2 M ammonium chloride, vapor diffusion, sitting drop, temperature 293K
Resolution 1.75 Å R-free 0.223
4U7T Crystal structure of DNMT3A-DNMT3L in complex with histone H3 Deposited 2014-07-31 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 F 2–13（12 aa）
Chain G 2–13（12 aa）
Not recorded ZN ZINC ION × 6 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1M Sodium Acetate, 0.6M Ammonium Sulfate
Resolution 2.90 Å R-free 0.261
4W5A Complex structure of ATRX ADD bound to H3K9me3S10ph peptide Deposited 2014-08-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–16（15 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；13-20% PEG 4000, 0.1 M MES, 3 mM MgCl2
Resolution 2.60 Å R-free 0.260
4W5A Complex structure of ATRX ADD bound to H3K9me3S10ph peptide Deposited 2014-08-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–16（15 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；13-20% PEG 4000, 0.1 M MES, 3 mM MgCl2
Resolution 2.60 Å R-free 0.260
4W5A Complex structure of ATRX ADD bound to H3K9me3S10ph peptide Deposited 2014-08-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 2–16（15 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；13-20% PEG 4000, 0.1 M MES, 3 mM MgCl2
Resolution 2.60 Å R-free 0.260
5B32 The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.3. Deposited 2016-02-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.35 Å R-free 0.259
5B33 The crystal structure of the H2AZ nucleosome with H3.3. Deposited 2016-02-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.92 Å R-free 0.252
5BNV Crystal structure of Human MCM2 HBD chaperoning a histone H3-H4 tetramer 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 × 6 PDB declaration: hexameric
Chain A 58–136（79 aa） Fragment：UNP residues 58-136
Chain D 58–136（79 aa） Fragment：UNP residues 58-136
Not recorded PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；1.5 M sodium/potassium phosphate, pH 8.0
Resolution 2.79 Å R-free 0.220
5BNX Crystal structure of Human MCM2 HBD and ASF1b chaperoning a histone H3.3-H4 dimer Deposited 2015-05-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 58–136（79 aa） Fragment：UNP residues 58-136
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 2.31 Å R-free 0.213
5DWQ Crystal structure of CARM1, sinefungin, and methylated H3 peptide (R17) Deposited 2015-09-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 14–31（18 aa） Fragment：UNP residues 14-31
Non-standard monomer：Yes (specific site not provided by mmCIF) SFG SINEFUNGIN × 2 GOL GLYCEROL × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.2 M Ammonium Sulfate, 0.1 M Tris pH 8.5, 18% w/v PEG 3350
Resolution 2.36 Å R-free 0.257
5DWQ Crystal structure of CARM1, sinefungin, and methylated H3 peptide (R17) Deposited 2015-09-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 14–31（18 aa） Fragment：UNP residues 14-31
Non-standard monomer：Yes (specific site not provided by mmCIF) SFG SINEFUNGIN × 2 GOL GLYCEROL × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.2 M Ammonium Sulfate, 0.1 M Tris pH 8.5, 18% w/v PEG 3350
Resolution 2.36 Å R-free 0.257
5DX0 Crystal structure of CARM1, sinefungin, and H3 peptide (R17) Deposited 2015-09-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 14–31（18 aa） Fragment：UNP residues 14-31
Chain G 14–31（18 aa） Fragment：UNP residues 14-31
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) SFG SINEFUNGIN × 2 GOL GLYCEROL × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.2 M Ammonium Sulfate, 0.1 M Tris pH 8.5, 18% w/v PEG 3350
Resolution 2.05 Å R-free 0.263
5DX0 Crystal structure of CARM1, sinefungin, and H3 peptide (R17) Deposited 2015-09-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain H 14–31（18 aa） Fragment：UNP residues 14-31
Chain I 14–31（18 aa） Fragment：UNP residues 14-31
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) SFG SINEFUNGIN × 2 GOL GLYCEROL × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.2 M Ammonium Sulfate, 0.1 M Tris pH 8.5, 18% w/v PEG 3350
Resolution 2.05 Å R-free 0.263
5JA4 Crystal structure of human TONSL and MCM2 HBDs binding to a histone H3-H4 tetramer Deposited 2016-04-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 58–136（79 aa）
Not recorded MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；298 K；0.1M MES pH 5.6, 7% isopropanol
Resolution 2.42 Å R-free 0.246
5JJY Crystal structure of SETD2 bound to histone H3.3 K36M peptide Deposited 2016-04-25 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 30–43（14 aa） Fragment：H3 peptide, UNP residues 30-43
Mutation：K36M ZN ZINC ION × 3 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SCN THIOCYANATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.2 M KSCN, 0.1 M Bis-Tris Propane, 20% PEG3350
Resolution 2.05 Å R-free 0.213
5JLB Crystal structure of SETD2 bound to histone H3.3 K36I peptide Deposited 2016-04-26 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 30–43（14 aa） Fragment：H3 peptide, UNP residues 30-43
Mutation：K36I SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SCN THIOCYANATE ION × 3 GOL GLYCEROL × 2 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.2 M KSCN, 0.1 M Bis-Tris Propane, 20% PEG3350
Resolution 1.50 Å R-free 0.190
5KDM Crystal structure of EBV tegument protein BNRF1 in complex with histone chaperone DAXX and histones H3.3-H4 Deposited 2016-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 2–136（135 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；0.1M MES pH 6.0, 0.8 M ammonium sulfate
Resolution 3.50 Å R-free 0.280
5X7X The crystal structure of the nucleosome containing H3.3 at 2.18 angstrom resolution Deposited 2017-02-27 Different construct Different 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 × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.18 Å R-free 0.256
6A5L RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA Deposited 2018-06-24 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 × 20 PDB declaration: 25-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.60 Å
6A5O RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome Deposited 2018-06-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.90 Å
6A5P RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome Deposited 2018-06-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å
6A5R RNA polymerase II elongation complex stalled at SHL(-2) of the nucleosome Deposited 2018-06-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
6A5T RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome Deposited 2018-06-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.70 Å
6A5U RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation Deposited 2018-06-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
6HGT Crystal structure of human KDM4A complexed with co-substrate analog NOG and histone H3 peptide with K9R mutation Deposited 2018-08-23 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 E 4–18（15 aa）
Mutation：K9R ZN ZINC ION × 2 OGA N-OXALYLGLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Co-substrate analog NOG and H3R9 peptide were co-crystallised with the protein.
Resolution 2.33 Å R-free 0.280
6HGT Crystal structure of human KDM4A complexed with co-substrate analog NOG and histone H3 peptide with K9R mutation Deposited 2018-08-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 4–18（15 aa）
Mutation：K9R ZN ZINC ION × 2 OGA N-OXALYLGLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Co-substrate analog NOG and H3R9 peptide were co-crystallised with the protein.
Resolution 2.33 Å R-free 0.280
6HGT Crystal structure of human KDM4A complexed with co-substrate analog NOG and histone H3 peptide with K9R mutation Deposited 2018-08-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 4–18（15 aa）
Mutation：K9R ZN ZINC ION × 2 OGA N-OXALYLGLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Co-substrate analog NOG and H3R9 peptide were co-crystallised with the protein.
Resolution 2.33 Å R-free 0.280
6HGT Crystal structure of human KDM4A complexed with co-substrate analog NOG and histone H3 peptide with K9R mutation Deposited 2018-08-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 4–18（15 aa）
Mutation：K9R ZN ZINC ION × 2 OGA N-OXALYLGLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Co-substrate analog NOG and H3R9 peptide were co-crystallised with the protein.
Resolution 2.33 Å R-free 0.280
6INQ RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position) Deposited 2018-10-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
6IR9 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome Deposited 2018-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6J4W RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-5) of the nucleosome Deposited 2019-01-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.90 Å
6J4X RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1A) Deposited 2019-01-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Y RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1B) Deposited 2019-01-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Z RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2019-01-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-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 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6J50 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome (tilted conformation) Deposited 2019-01-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-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 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
6J51 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome, weak Elf1 (+1 position) Deposited 2019-01-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6PZV Crystal Structure of Bovine DNMT1 RFTS domain in complex with H3K9me3 and Ubiquitin Deposited 2019-08-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 2–27（26 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) FLC CITRATE ANION × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.5；277 K；0.1M citric acid (pH 3.5), 28% PEG8000
Resolution 3.01 Å R-free 0.272
6PZV Crystal Structure of Bovine DNMT1 RFTS domain in complex with H3K9me3 and Ubiquitin Deposited 2019-08-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain H 2–27（26 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.5；277 K；0.1M citric acid (pH 3.5), 28% PEG8000
Resolution 3.01 Å R-free 0.272
6R0C Human-D02 Nucleosome Core Particle with biotin-streptavidin label Deposited 2019-03-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded MN MANGANESE (II) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6RNY PFV intasome - nucleosome strand transfer complex Deposited 2019-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: octadecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE；1 min incubation 3.5s blot
Resolution 3.90 Å
6U04 Crystal structure of human BRPF1 PZP bound to histone H3 tail Deposited 2019-08-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–13（12 aa）
Not recorded PR PRASEODYMIUM ION × 1 ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291.15 K；0.2 M Lithium sulfate, 0.1 M Tris-HCl pH 8.5, 40% (v/v) PEG400, and 0.01M Praseodymium(III) acetate hydrate
Resolution 2.20 Å R-free 0.208
7A08 CryoEM Structure of cGAS Nucleosome complex Deposited 2020-08-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain d 2–136（135 aa）
Chain h 2–136（135 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.11 Å
7CIZ Crystal structure of DNAJC9 HBD helix2 in complex with H3.3-H4 dimer and MCM2 HBD Deposited 2020-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 58–136（79 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.05 M Lithium sulfate, 0.05 M Sodium sulfate; 0.05 M Tris, pH 8.5, 30% (v/v) PEG400.
Resolution 1.80 Å R-free 0.214
7CIZ Crystal structure of DNAJC9 HBD helix2 in complex with H3.3-H4 dimer and MCM2 HBD Deposited 2020-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 58–136（79 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.05 M Lithium sulfate, 0.05 M Sodium sulfate; 0.05 M Tris, pH 8.5, 30% (v/v) PEG400.
Resolution 1.80 Å R-free 0.214
7CIZ Crystal structure of DNAJC9 HBD helix2 in complex with H3.3-H4 dimer and MCM2 HBD Deposited 2020-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain I 58–136（79 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.05 M Lithium sulfate, 0.05 M Sodium sulfate; 0.05 M Tris, pH 8.5, 30% (v/v) PEG400.
Resolution 1.80 Å R-free 0.214
7CJ0 Crystal structure of DNAJC9 HBD in complex with H3.3-H4 dimer and MCM2 HBD Deposited 2020-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 58–136（79 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.17 M Sodium acetate, 0.1 M Tris, pH8.5, 25% (v/v) PEG 4000, 20% (v/v) Glycerol
Resolution 2.50 Å R-free 0.295
7CJ0 Crystal structure of DNAJC9 HBD in complex with H3.3-H4 dimer and MCM2 HBD Deposited 2020-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 58–136（79 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.17 M Sodium acetate, 0.1 M Tris, pH8.5, 25% (v/v) PEG 4000, 20% (v/v) Glycerol
Resolution 2.50 Å R-free 0.295
7CWH Structural basis of RACK7 PHD to read a pediatric glioblastoma-associated histone mutation H3.3G34R Deposited 2020-08-28 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 32–42（11 aa）
Mutation：G34R ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7.4；293 K；Ionic strength (raw mmCIF value) 500；Pressure 1
NMR sample composition 0.7 mM [U-13C; U-15N] RACK7 PHD, 1.4 mM H3.3G34R, 100 mM sodium chloride, 0.02 % w/v sodium azide, 50 mM sodium phosphate, 2 mM [U-2H] DDT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.7 mM [U-13C; U-15N] RACK7 PHD, 1.4 mM H3.3G34R, 100 mM sodium chloride, 0.02 % w/v sodium azide, 50 mM sodium phosphate, 2 mM [U-2H] DTT, 100% D2O | 100% D2O
NMR sample composition 1 mM [U-13C; U-15N] G34R, 1.2 mM RACK7 PHD, 100 mM sodium chloride, 0.02 % w/v sodium azide, 50 mM sodium phosphate, 2 mM [U-2H] DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
7OKP Crystal structure of mouse CARM1 in complex with histone H3_13-22 K18 acetylated Deposited 2021-05-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 14–23（10 aa）
Chain F 14–23（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) MLI MALONATE ION × 2 QVR (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[(~{E})-prop-1-enyl]oxolane-3,4-diol × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1M sodium malonate, 0.1M MES pH7.0, 0.2M sodium chloride
Resolution 2.20 Å R-free 0.254
7OKP Crystal structure of mouse CARM1 in complex with histone H3_13-22 K18 acetylated Deposited 2021-05-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain G 14–23（10 aa）
Chain H 14–23（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) MLI MALONATE ION × 8 QVR (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[(~{E})-prop-1-enyl]oxolane-3,4-diol × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1M sodium malonate, 0.1M MES pH7.0, 0.2M sodium chloride
Resolution 2.20 Å R-free 0.254
7V1L Structure of sNASP core in complex with H3 alpha3 helix peptide Deposited 2021-08-04 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 V 117–136（20 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.4M Na-K phosphate, pH 8.2
Resolution 2.85 Å R-free 0.246
7V1M Structural basis for the co-chaperone relationship of sNASP and ASF1b Deposited 2021-08-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 2–136（135 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；8% v/v Tacsimate, pH 6.0, 20% w/v PEG 3350
Resolution 2.83 Å R-free 0.240
7V1M Structural basis for the co-chaperone relationship of sNASP and ASF1b Deposited 2021-08-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 2–136（135 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；8% v/v Tacsimate, pH 6.0, 20% w/v PEG 3350
Resolution 2.83 Å R-free 0.240
7VCQ structure of viral protein BKRF4 in complex with H3.3-H4-ASF1 Deposited 2021-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 58–136（79 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2% Tacsimate pH 7.0; o.1M HEPES pH 7.5; 20% PEG3350
Resolution 3.00 Å R-free 0.283
7VCQ structure of viral protein BKRF4 in complex with H3.3-H4-ASF1 Deposited 2021-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 58–136（79 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2% Tacsimate pH 7.0; o.1M HEPES pH 7.5; 20% PEG3350
Resolution 3.00 Å R-free 0.283
7VCQ structure of viral protein BKRF4 in complex with H3.3-H4-ASF1 Deposited 2021-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 58–136（79 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2% Tacsimate pH 7.0; o.1M HEPES pH 7.5; 20% PEG3350
Resolution 3.00 Å R-free 0.283
7W5M Crystal structure of AtNASP in complex of H3 alpha3 helix peptide Deposited 2021-11-30 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 117–136（20 aa）
Not recorded GOL GLYCEROL × 1 PG4 TETRAETHYLENE GLYCOL × 2 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；20% PEG 300, 0.2M Ammonium sulfate, 0.1M Phosphate citrate, pH 4.2, 10% Glycerol
Resolution 2.15 Å R-free 0.227
7WBV RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome Deposited 2021-12-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7WBW RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3.5) of the nucleosome Deposited 2021-12-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.10 Å
7WBX RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome Deposited 2021-12-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7XSE RNA polymerase II elongation complex transcribing a nucleosome (EC42) Deposited 2022-05-13 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 × 30 PDB declaration: 33-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7XSX RNA polymerase II elongation complex transcribing a nucleosome (EC49) Deposited 2022-05-15 Different construct Different 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 × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7XSZ RNA polymerase II elongation complex transcribing a nucleosome (EC115) Deposited 2022-05-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7XT7 RNA polymerase II elongation complex transcribing a nucleosome (EC49B) Deposited 2022-05-16 Different construct Different 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 × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7XTD RNA polymerase II elongation complex transcribing a nucleosome (EC58oct) Deposited 2022-05-16 Different construct Different 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 × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7XTI RNA polymerase II elongation complex transcribing a nucleosome (EC58hex) Deposited 2022-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8JH2 RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.70 Å
8JH3 RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8JH4 RNA polymerase II elongation complex containing 60 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9B3P The cryo-EM structure of the H2A.Z-H3.3 double-variant nucleosome Deposited 2024-03-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20mM Tris-HCl, 5mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE；Freezing condition: blot force 0, blot time 4.5 second
Resolution 3.00 Å
9EOZ Human OGG1 bound to a nucleosome core particle with 8-oxodGuo lesion at SHL6.0 Deposited 2024-03-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain E 2–136（135 aa）
Chain K 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 3.10 Å
9II7 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome containing histone variant H2A.B Deposited 2024-06-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9J0N Paused elongation complex of mammalian RNA polymerase II with nucleosome (PEC2-nuc) Deposited 2024-08-02 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 × 27 PDB declaration: 30-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 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9J0O Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC1-nuc) Deposited 2024-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-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 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9J0P Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC2-nuc) Deposited 2024-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-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 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9L1X hDEK-nucleosome complex (conformation 1) Deposited 2024-12-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded UNX UNKNOWN LIGAND × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.69 Å
9L22 hDEK-nucleosome complex (conformation 2) Deposited 2024-12-16 Different construct Different 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 UNX UNKNOWN LIGAND × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9UTH DPF3b in complex with H3K14cr peptide Deposited 2025-05-03 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 B 2–27（26 aa）
Chain D 2–27（26 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；4 M Sodium Formate, pH 7.0
Resolution 2.69 Å R-free 0.230
9UTH DPF3b in complex with H3K14cr peptide Deposited 2025-05-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 2–27（26 aa）
Chain H 2–27（26 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；4 M Sodium Formate, pH 7.0
Resolution 2.69 Å R-free 0.230
9WMS Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type B) Deposited 2025-09-03 Different construct Different 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）
Mutation：K36M Mutation：K36M ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9WMT Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type A) Deposited 2025-09-03 Different construct Different 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）
Mutation：K36M Mutation：K36M ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
9WMU Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type A) Deposited 2025-09-03 Different construct Different 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）
Mutation：K36M Mutation：K36M ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.28 Å
9WMV Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type B) Deposited 2025-09-03 Different construct Different 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 × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.66 Å
9WMW Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, FACT-hexamer) Deposited 2025-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different 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 × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å

94 other PDB entries and 122 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H33_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–11； UniProt 2–12 Author chain D； PDBConstruct 1–11； UniProt 2–12

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 4tmp

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4tmp
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4tmp
Deposition date deposition_date2014-06-02
Structure title titleCrystal structure of AF9 YEATS bound to H3K9ac peptide
Keywords keywordstranscription, complex, histone modification, immunoglobin fold; TRANSCRIPTION
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_guinier30.20 Å
Radius of gyration Rg (electron density) rg_electron30.51 Å
Forward intensity I(0) i019709200.00
Molecular weight molecular_weight34913.0 kDa
Excluded volume excluded_volume43948 ų
Envelope volume envelope_volume57411 ų
Hydration-shell volume shell_volume18061 ų
Envelope diameter envelope_diameter115.2 Å
Shell Rg shell_rg32.66 Å
Envelope Rg envelope_rg30.80 Å
Shape Rg shape_rg30.55 Å
Total Rg total_rg30.63 Å
Total atoms total_atoms4908
Residues n_residues293
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 dmax107.9 Å
Rg (real space) rg_real30.75 Å
Rg uncertainty (real space) rg_real_error1.69 Å
I(0) (real space) i0_real1.9710e+07
I(0) uncertainty (real space) i0_real_error3.5420e+05
Rg (reciprocal space) rg_reciprocal30.52 Å
I(0) (reciprocal space) i0_reciprocal19710000.0000
Solution quality estimate total_estimate0.6855
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.7 Å
Skewness Skewness skewness0.580
Kurtosis Kurtosis kurtosis-0.543
Angular range angular_range— – 0.2600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4260000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.295; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.086; Smooth: 0.946
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id4tmpA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1970 — YEATS domain
Domain ID domain_id4tmpC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1970 — YEATS domain
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8. Citations (1)

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9. Files and Curves (10)