6mil

Crystal structure of AF9 YEATS domain in complex with histone H3K9bu

Method: X-RAY DIFFRACTION D_max: 107.4 Å Quality: REASONABLE

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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	Fragment：YEATS domain residues 1-138	Histone H3K9bu × 1 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–138	Fragment：YEATS domain residues 1-138	Histone H3K9bu × 1 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

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 6MIL	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 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 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
4TMP Crystal structure of AF9 YEATS bound to H3K9ac peptide Deposited 2014-06-02	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	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 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 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
6MIM Crystal structure of AF9 YEATS domain Y78W mutant in complex with histone H3K9cr Deposited 2018-09-19	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 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 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 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 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

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	6mil
Deposition date deposition_date	2018-09-19
Structure title title	Crystal structure of AF9 YEATS domain in complex with histone H3K9bu
Keywords keywords	Transcription, Epigenetic, Histone reader; TRANSCRIPTION
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	30.06 Å
Radius of gyration Rg (electron density) rg_electron	30.50 Å
Forward intensity I(0) i0	19340200.00
Molecular weight molecular_weight	34697.0 kDa
Excluded volume excluded_volume	43708 Å³
Envelope volume envelope_volume	56251 Å³
Hydration-shell volume shell_volume	17821 Å³
Envelope diameter envelope_diameter	113.7 Å
Shell Rg shell_rg	32.39 Å
Envelope Rg envelope_rg	30.76 Å
Shape Rg shape_rg	30.53 Å
Total Rg total_rg	30.61 Å
Total atoms total_atoms	2452
Residues n_residues	289
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	107.4 Å
Rg (real space) rg_real	30.62 Å
Rg uncertainty (real space) rg_real_error	1.37 Å
I(0) (real space) i0_real	1.9340e+07
I(0) uncertainty (real space) i0_real_error	3.1860e+05
Rg (reciprocal space) rg_reciprocal	30.39 Å
I(0) (reciprocal space) i0_reciprocal	19340000.0000
Solution quality estimate total_estimate	0.6849
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.3 Å
Skewness Skewness skewness	0.593
Kurtosis Kurtosis kurtosis	-0.516
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4589000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.292; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.099; Smooth: 0.930

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Protein AF-9
Molecular weight formula_weight	16611.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	2814

GSHMASSCAVQVKLELGHRAQVRKKPTVEGFTHDWMVFVRGPEHSNIQHFVEKVVFHLHESFPRPKRVCKDPPYKVEESGYAGFILPIEVYFKNKEEPRKVRFDYDLFLHLEGHPPVNHLRCEKLTFNNPTEDFRRKLLKA

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

Entity 2 Entity 2 polymer

Description description	Histone H3K9bu
Molecular weight formula_weight	2146.5 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

ARTKQTARXSTGGKAPRKQ

Entity 3 Entity 3 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MALONATE ION
Molecular weight formula_weight	102.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	342

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6milA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1970 — YEATS domain

Domain ID domain_id	6milC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1970 — YEATS domain

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8. Citations (1)

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Unit-cell length a length_a	123.989 Å
Unit-cell length b length_b	44.913 Å
Unit-cell length c length_c	70.804 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.54 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.930 Å
Low-resolution limit resolution_low	48.819 Å
R factor r_factor	0.1866
R_work r_work	0.1828
R_free r_free	0.2358

fit	/app/data/saxs_computation/mi/6mil/6mil.fit
pddf	/app/data/pr_computation/mi/6mil/6mil.pr.out
profile	/app/data/saxs_computation/mi/6mil/6mil.dat

Crystal structure of AF9 YEATS domain in complex with histone H3K9bu

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

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)