9im4

Crystal Structure of AF9 YEATS domain F28R mutant in complex with histone H3K9la

Method: X-RAY DIFFRACTION D_max: 77.2 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein AF-9

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–138	Mutation：F28R	Histone H3.3C × 1 （Q6NXT2）	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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–138	Mutation：F28R	Histone H3.3C × 1 （Q6NXT2）	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

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 9IM4	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 mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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
4TMP Crystal structure of AF9 YEATS bound to H3K9ac peptide Deposited 2014-06-02	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） Fragment：YEATS domain (UNP residues 1-138)	Not recorded	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
4TMP Crystal structure of AF9 YEATS bound to H3K9ac peptide Deposited 2014-06-02	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 C 1–138（138 aa） Fragment：YEATS domain (UNP residues 1-138)	Not recorded	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
5HJB AF9 YEATS in complex with histone H3 Crotonylation at K9 Deposited 2016-01-12	Different construct Different mutation/modification 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 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）	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 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）	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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 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	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 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	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 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 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 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）	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 mutation/modification 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 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）	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 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）	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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 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 mutation/modification 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 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 mutation/modification Different oligomeric state 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 mutation/modification 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 mutation/modification 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 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） 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 mutation/modification Different ligand/ion 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 mutation/modification 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

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 21–158； UniProt 1–138 Author chain B； PDBConstruct 21–158； UniProt 1–138

Histone H3.3C

OrganismNot specified

UniProt Q6NXT2

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 P； UniProt 2–11	Non-standard monomer：Yes (specific site not provided by mmCIF)	Protein AF-9 × 1 （P42568）	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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 2–11	Non-standard monomer：Yes (specific site not provided by mmCIF)	Protein AF-9 × 1 （P42568）	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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9IM4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
21GE Solution structures of BRD9 bromodomain in complex with histone H3 acetyl-lysine 18 (H3K18ac) peptide Deposited 2025-12-11	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 12–26（15 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) Null；Pressure 1 NMR sample composition 500 mM sodium chloride, 2.7 mM potassium chloride, 10 mM sodium phosphate, 1.8 mM potassium phosphate, 2 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 500 mM sodium chloride, 2.7 mM potassium chloride, 10 mM sodium phosphate, 1.8 mM potassium phosphate, 2 mM DTT, 100% D2O \| 100% D2O	Resolution not provided
21HJ Solution structures of BRD9 bromodomain in complex with histone H3 lactyl-lysine 18 (H3K18la) peptide Deposited 2025-12-12	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 12–26（15 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) null；Pressure 1 NMR sample composition 500 mM sodium chloride, 2.7 mM potassium chloride, 10 mM sodium phosphate, 1.8 mM potassium phosphate, 2 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 500 mM sodium chloride, 2.7 mM potassium chloride, 10 mM sodium phosphate, 1.8 mM potassium phosphate, 2 mM DTT, 100% D2O \| 100% D2O	Resolution not provided
3KV4 Structure of PHF8 in complex with histone H3 Deposited 2009-11-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–25（24 aa） Fragment：UNP Residues 2-25	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2 FE2 FE (II) ION × 1 NI NICKEL (II) ION × 1 EDO 1,2-ETHANEDIOL × 13 OGA N-OXALYLGLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；25% (v/v) polyethylene glycol 3350, 0.2 M NaCl, and 0.1 M NaCitrate pH 5.6, VAPOR DIFFUSION, HANGING DROP	Resolution 2.19 Å R-free 0.255
4Z5T The nucleosome containing human H3.5 Deposited 2015-04-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain A 1–135（135 aa） Chain E 1–135（135 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride	Resolution 2.80 Å R-free 0.269
7W67 The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me0 peptide Deposited 2021-12-01	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 M 2–10（9 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3350	Resolution 2.19 Å R-free 0.222
7W6I The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me1 peptide Deposited 2021-12-01	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 B 2–10（9 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3,350	Resolution 2.56 Å R-free 0.244
7W6J The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me2 peptide Deposited 2021-12-01	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 B 2–10（9 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3350	Resolution 2.68 Å R-free 0.252
7W6L The crystal structure of MLL3-RBBP5-ASH2L in complex with H3K4me0 peptide Deposited 2021-12-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain M 2–10（9 aa）	Not recorded	ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；100 mM sodium cacodylate, pH 6.5, 10% polyethylene glycol 3350, 0.1 M MgCl2	Resolution 2.26 Å R-free 0.223
8Q1G LSD1-CoREST bound to Acetylated K14 of Histone H3 Deposited 2023-07-31	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 C 2–22（21 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Sodium Tartrate 1.2M, ADA 0.1M,	Resolution 2.60 Å R-free 0.255
8Q1H LSD1 Y391K-CoREST bound to Histone H3 N-terminal tail Deposited 2023-07-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 2–22（21 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Sodium Tartrate 1.2 M, ADA 0.1M	Resolution 2.90 Å R-free 0.254
8Q1J LSD1 Y391K-CoREST bound to Acetylated K14 of Histone H3 Deposited 2023-07-31	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 C 2–22（21 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Sodium Tartate 1.2 M, ADA 0.1M	Resolution 2.87 Å R-free 0.272
8RBX Structure of Integrator-PP2A bound to a paused RNA polymerase II-DSIF-NELF-nucleosome complex Deposited 2023-12-05	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 × 43 PDB declaration: 46-meric	Chain M 1–135（135 aa） Chain S 1–135（135 aa）	Not recorded	ZN ZINC ION × 10 MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
8SR6 Crystal structure of legAS4 from Legionella pneumophila subsp. pneumophila with histone H3 (3-17)peptide Deposited 2023-05-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 4–18（15 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1M Bis-Tris 6.5 and 38% PPG P400	Resolution 2.22 Å R-free 0.230
8T4F Transporter associated with antigen processing (TAP) bound to the 9-mer peptide RRYQKSTEL Deposited 2023-06-09	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 52–60（9 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8VLD Crystal structure of Ash1L PHD finger in complex with histone H3K4me2 Deposited 2024-01-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain P 2–12（11 aa） Chain T 2–12（11 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) 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；277 K；1.6 M sodium citrate pH 6.5	Resolution 1.92 Å R-free 0.249
8VLF Crystal structure of Ash1L PHD finger in complex with histone H3K4me3 Deposited 2024-01-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain P 2–13（12 aa） Chain T 2–13（12 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；1.6 M sodium citrate pH 6.5	Resolution 1.34 Å R-free 0.188
8Z73 Crystal Structure of AF9 in complex with H3K9la peptide Deposited 2024-04-19	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 2–11（10 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2–11（10 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 2–11（10 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 2–11（10 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	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
8ZXC NMR solution structures of ASH1L BRD-PHD domain in complex with H3K4me2 peptide Deposited 2024-06-14	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 2–13（12 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) null；Pressure 1 NMR sample composition 100 mM sodium phosphate, 2 mM DTT, 50 mM potassium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 100 mM sodium phosphate, 2 mM DTT, 50 mM potassium chloride, 100% D2O \| 100% D2O	Resolution not provided
9C0O Crystal structure of DmCfp1 PHD finger bound to H3K4me3 Deposited 2024-05-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 2–16（15 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	DMS DIMETHYL SULFOXIDE × 1 ZN ZINC ION × 3 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；15% PEG3350, 0.01M Tris pH8.5, 0.2M Ammonium sulfate	Resolution 1.53 Å R-free 0.194
9DZN KAT6A MYST domain complexed with a H3K14-CoA bisubstrate inhibitor Deposited 2024-10-16	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 C 6–24（19 aa）	Not recorded	CMC CARBOXYMETHYL COENZYME A × 1 ZN ZINC ION × 1 GOL* GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；294.15 K；1.25 M NH4SO4, 0.28 M NaCl, and 0.1 M HEPES pH 6.4	Resolution 1.72 Å R-free 0.245
9N61 Transporter associated with antigen processing (TAP) bound to the 9-mer peptide RRYQKSTEL and ATP Deposited 2025-02-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 52–60（9 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9V5M The crystal structure of RBBP4-H3 complex Deposited 2025-05-26	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 2–15（14 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å R-free 0.211

22 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	H3C_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–10； UniProt 2–11 Author chain P； PDBConstruct 1–10； UniProt 2–11

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9im4
Deposition date deposition_date	2024-07-02
最后修订 last_revision	2025-07-09
Structure title title	Crystal Structure of AF9 YEATS domain F28R mutant in complex with histone H3K9la
Keywords keywords	YEATS domain, PEPTIDE BINDING PROTEIN; PEPTIDE BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	23.94 Å
Radius of gyration Rg (electron density) rg_electron	22.98 Å
Forward intensity I(0) i0	40031900.00
Molecular weight molecular_weight	32515.0 kDa
Excluded volume excluded_volume	31337 Å³
Envelope volume envelope_volume	57929 Å³
Hydration-shell volume shell_volume	21337 Å³
Envelope diameter envelope_diameter	81.9 Å
Shell Rg shell_rg	29.27 Å
Envelope Rg envelope_rg	22.88 Å
Shape Rg shape_rg	22.93 Å
Total Rg total_rg	23.67 Å
Total atoms total_atoms	2473
Residues n_residues	294
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	77.2 Å
Rg (real space) rg_real	23.83 Å
Rg uncertainty (real space) rg_real_error	0.61 Å
I(0) (real space) i0_real	4.0030e+07
I(0) uncertainty (real space) i0_real_error	5.3220e+05
Rg (reciprocal space) rg_reciprocal	23.86 Å
I(0) (reciprocal space) i0_reciprocal	40030000.0000
Solution quality estimate total_estimate	0.8988
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	35.0 Å
Skewness Skewness skewness	0.104
Kurtosis Kurtosis kurtosis	-0.632
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6962000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.974

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Protein AF-9
Molecular weight formula_weight	18510.3 kDa
Mutation mutation	F28R
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2474

MGSSHHHHHHSSGLVPRGSHMASSCAVQVKLELGHRAQVRKKPTVEGRTHDWMVFVRGPEHSNIQHFVEKVVFHLHESFPRPKRVCKDPPYKVEESGYAGFILPIEVYFKNKEEPRKVRFDYDLFLHLEGHPPVNHLRCEKLTFNNPTEDFRRKLLKA

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Histone H3.3C
Molecular weight formula_weight	1221.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,C

ARTKQTARXS

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1

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8. Citations (1)

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Unit-cell length a length_a	83.081 Å
Unit-cell length b length_b	83.081 Å
Unit-cell length c length_c	116.259 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.794 Å
Low-resolution limit resolution_low	30.591 Å
R factor r_factor	0.2711
R_work r_work	0.2660
R_free r_free	0.3150

fit	/app/data/saxs_computation/im/9im4/9im4.fit
pddf	/app/data/pr_computation/im/9im4/9im4.pr.out
profile	/app/data/saxs_computation/im/9im4/9im4.dat

Crystal Structure of AF9 YEATS domain F28R mutant in complex with histone H3K9la

1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein AF-9

State in the Current Structure

Other States of the Same Protein in the Database

Histone H3.3C

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)