6p39

Crystal Structure Analysis of TAF1 Bromodomain

Method: X-RAY DIFFRACTION D_max: 61.3 Å Quality: GOOD

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

Transcription initiation factor TFIID subunit 1

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1521–1656	Not recorded	NQY 3-methoxy-4-{[(6aR)-5-methyl-6-oxo-6,6a,7,8,9,10-hexahydro-5H-dipyrido[1,2-a:3',2'-e]pyrazin-2-yl]amino}-N-(1-methylpiperidin-4-yl)benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；PEG1000, Tris pH 8.0	Resolution 2.94 Å R-free 0.212

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 6P39	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EQF CRYSTAL STRUCTURE OF THE DOUBLE BROMODOMAIN MODULE FROM HUMAN TAFII250 Deposited 2000-04-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1359–1638（280 aa） Fragment：DOUBLE BROMODOMAIN, RESIDUES 1359-1638	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；294 K；ammonium sulfate, TrisCl, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.10 Å R-free 0.246
3AAD Structure of the histone chaperone CIA/ASF1-double bromodomain complex linking histone modifications and site-specific histone eviction Deposited 2009-11-16	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 A 1342–1629（288 aa） Fragment：Bromodomain	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.65；293 K；0.1M MES, 1.1M AMMONIUM SULFATE, 0.25M LITHIUM SULFATE, pH 5.65, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.293
3UV4 Crystal Structure of the second bromodomain of human Transcription initiation factor TFIID subunit 1 (TAF1) Deposited 2011-11-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1501–1635（135 aa） Fragment：unp residues 1501-1635	Not recorded	EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.056M NaH2PO4 1.344M K2HPO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.89 Å
3UV4 Crystal Structure of the second bromodomain of human Transcription initiation factor TFIID subunit 1 (TAF1) Deposited 2011-11-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1501–1635（135 aa） Fragment：unp residues 1501-1635	Not recorded	EDO 1,2-ETHANEDIOL × 2 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.056M NaH2PO4 1.344M K2HPO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.89 Å
3UV5 Crystal Structure of the tandem bromodomains of human Transcription initiation factor TFIID subunit 1 (TAF1) Deposited 2011-11-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1373–1635（263 aa） Fragment：unp residues 1373-1635	Not recorded	TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；0.1M Tris-HCl, 1.1M (NH4)2SO4, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.03 Å R-free 0.230
4RGW Crystal Structure of a TAF1-TAF7 Complex in Human Transcription Factor IID Deposited 2014-09-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 579–1215（637 aa） Fragment：DUF3591 domain, UNP residues 579-1215	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；0.2 M potassium sodium tartrate tetrahydrate, pH 7.4, 20% w/v PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.234
4YYM Crystal structure of TAF1 BD2 Bromodomain bound to a butyryllysine peptide Deposited 2015-03-24	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 1497–1638（142 aa） Fragment：bromodomain (UNP residues 1497-1638) Chain B 1497–1638（142 aa） Fragment：bromodomain (UNP residues 1497-1638)	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M calcium chloride, 20 w/v PEG3350	Resolution 1.50 Å R-free 0.261
4YYN Crystal structure of TAF1 BD2 Bromodomain bound to a crotonyllysine peptide Deposited 2015-03-24	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 1497–1638（142 aa） Fragment：bromodomain (UNP residues 1497-1638) Chain B 1497–1638（142 aa） Fragment：bromodomain (UNP residues 1497-1638)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M calcium acetate, 20% w/v PEG3350	Resolution 1.85 Å R-free 0.243
5FUR Structure of human TFIID-IIA bound to core promoter DNA Deposited 2016-01-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain G 1–1872（1872 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 10 MM HEPES, 10 MM MGCL2, 50 MM KCL, 3% TREHALOSE 1 MM DTT, 0.0125% NP-40；pH 7.9；10 MM HEPES, 10 MM MGCL2, 50 MM KCL, 3% TREHALOSE 1 MM DTT, 0.0125% NP-40 cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE	Resolution 8.50 Å
5I1Q Second bromodomain of TAF1 bound to a pyrrolopyridone compound Deposited 2016-01-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1497–1638（142 aa） Fragment：second bromodomain (UNP residues 1497-1638)	Not recorded	67C 3-[6-(but-3-en-1-yl)-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl]-N,N-dimethylbenzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M ammonium nitrate, 20% PEG3350	Resolution 1.50 Å R-free 0.214
5I29 TAF1(2) bound to a pyrrolopyridone compound Deposited 2016-02-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1497–1638（142 aa） Fragment：second bromodomain (UNP residues 1497-1638)	Not recorded	67B N,N-dimethyl-3-(6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)benzamide × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M calcium chloride, 20% PEG3350	Resolution 1.21 Å R-free 0.216
5MG2 Crystal structure of the second bromodomain of human TAF1 in complex with BAY-299 chemical probe Deposited 2016-11-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1501–1635（135 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 3 7M8 6-(3-oxidanylpropyl)-2-(1,3,6-trimethyl-2-oxidanylidene-benzimidazol-5-yl)benzo[de]isoquinoline-1,3-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277.15 K；20%PEG 10K, 0.20 M NaCl, 0.1M citrate/phosphate pH 4.2	Resolution 1.75 Å R-free 0.220
6BQD TAF1-BD2 bromodomain in complex with (E)-3-(6-(but-2-en-1-yl)-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)-N,N-dimethylbenzamide Deposited 2017-11-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1501–1630（130 aa） Fragment：TAF1-BD2 bromodomain	Not recorded	69G 3-{6-[(2E)-but-2-en-1-yl]-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl}-N,N-dimethylbenzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5；277 K；8% Tacsimate pH 5.0 and 20% PEG3350	Resolution 2.14 Å R-free 0.226
6BQD TAF1-BD2 bromodomain in complex with (E)-3-(6-(but-2-en-1-yl)-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)-N,N-dimethylbenzamide Deposited 2017-11-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1501–1630（130 aa） Fragment：TAF1-BD2 bromodomain	Not recorded	69G 3-{6-[(2E)-but-2-en-1-yl]-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl}-N,N-dimethylbenzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5；277 K；8% Tacsimate pH 5.0 and 20% PEG3350	Resolution 2.14 Å R-free 0.226
6FIC Bivalent Inhibitor UNC4512 Bound to the TAF1 Bromodomain Tandem Deposited 2018-01-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain T 1359–1638（280 aa）	Not recorded	DKH 3-azanyl-2-[3-[2-[2-[2-[2-[2-[2-[2-[2-[2-[2-[2-[2-[2-[2-[2-[2-[2-[[3-azanyl-1-[[2-[[3-methyl-6-[4-methyl-3-(methylsulfonyl-$l^{2}-azanyl)cyclohexa-1,3,5-trien-1-yl]-[1,2,4]triazolo[4,3-b]pyridazin-8-yl]-$l^{2}-azanyl]-2-oxidanylidene-ethyl]amino]-1-oxidanylidene-propan-2-yl]amino]-2-oxidanylidene-ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]propanoylamino]-~{N}-[3-[[3-methyl-6-[4-methyl-3-(methylsulfonylamino)phenyl]-[1,2,4]triazolo[4,3-b]pyridazin-8-yl]amino]-3-oxidanylidene-propyl]propanamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M HEPES pH 7.5, 4.2 M NaCl	Resolution 2.18 Å R-free 0.236
6MZD Human TFIID Lobe A canonical Deposited 2018-11-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 21–1893（1873 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE；BT 4s; BF 15N	Resolution 9.80 Å
6MZL Human TFIID canonical state Deposited 2018-11-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 22 PDB declaration: 22-meric	Chain A 1–1872（1872 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE；BT 4s; BF 15N	Resolution 23.00 Å
6P38 Crystal Structure Analysis of TAF1 Bromodomain Deposited 2019-05-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1522–1656（135 aa）	Not recorded	NQV 4-{[(3R)-4-cyclopentyl-1,3-dimethyl-2-oxo-1,2,3,4-tetrahydropyrido[2,3-b]pyrazin-6-yl]amino}-N-(1-methylpiperidin-4-yl)-3-[(propan-2-yl)oxy]benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 2000, Trimethylamine N-oxide dihydrate, Tris pH 8.5	Resolution 2.80 Å R-free 0.219
6P3A Crystal Structure Analysis of TAF1 Bromodomain Deposited 2019-05-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1522–1656（135 aa）	Not recorded	NQP 4-{[(3R)-1-(but-3-en-1-yl)-3-methyl-4-(oxan-4-yl)-2-oxo-1,2,3,4-tetrahydropyrido[2,3-b]pyrazin-6-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG8000, Tris pH 8.0	Resolution 2.99 Å R-free 0.286
6P3A Crystal Structure Analysis of TAF1 Bromodomain Deposited 2019-05-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1522–1656（135 aa）	Not recorded	NQP 4-{[(3R)-1-(but-3-en-1-yl)-3-methyl-4-(oxan-4-yl)-2-oxo-1,2,3,4-tetrahydropyrido[2,3-b]pyrazin-6-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG8000, Tris pH 8.0	Resolution 2.99 Å R-free 0.286
7EDX p53-bound TFIID-based core PIC on HDM2 promoter Deposited 2021-03-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 37 PDB declaration: 39-meric	Chain A 1–1872（1872 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 4.50 Å
7EG7 TFIID-based core PIC on SCP promoter Deposited 2021-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 37 PDB declaration: 39-meric	Chain A 1–1872（1872 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 6.20 Å
7EG8 TFIID-based core PIC on PUMA promoter Deposited 2021-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 37 PDB declaration: 39-meric	Chain A 1–1872（1872 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 7.40 Å
7EG9 TFIID-based intermediate PIC on SCP promoter Deposited 2021-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 39 PDB declaration: 41-meric	Chain A 1–1872（1872 aa）	Not recorded	ZN ZINC ION × 10 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
7EGA TFIID-based intermediate PIC on PUMA promoter Deposited 2021-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 39 PDB declaration: 41-meric	Chain A 1–1872（1872 aa）	Not recorded	ZN ZINC ION × 10 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
7EGB TFIID-based holo PIC on SCP promoter Deposited 2021-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric	Chain A 1–1872（1872 aa）	Not recorded	ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7EGC p53-bound TFIID-based holo PIC on HDM2 promoter Deposited 2021-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric	Chain A 1–1872（1872 aa）	Not recorded	ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
7EGD SCP promoter-bound TFIID-TFIIA in initial TBP-loading state Deposited 2021-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric	Chain A 1–1872（1872 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.75 Å
7EGE TFIID in canonical conformation Deposited 2021-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain A 1–1872（1872 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.00 Å
7EGH TFIID lobe C subcomplex Deposited 2021-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain A 1–1872（1872 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.04 Å
7EGI TFIID in rearranged conformation Deposited 2021-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 22 PDB declaration: 22-meric	Chain A 1–1872（1872 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.82 Å
7EGJ SCP promoter-bound TFIID-TFIIA in post TBP-loading state Deposited 2021-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric	Chain A 1–1872（1872 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.64 Å
7ENA TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre-hPIC-MED) Deposited 2021-04-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 74 PDB declaration: 76-meric	Chain DA 1–1872（1872 aa）	Not recorded	ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.07 Å
7ENC TFIID-based PIC-Mediator holo-complex in fully-assembled state (hPIC-MED) Deposited 2021-04-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 74 PDB declaration: 76-meric	Chain DA 1–1872（1872 aa）	Not recorded	ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.13 Å
7JJG Crystal structure of the second bromodomain (BD2) of human TAF1 bound to ATR kinase inhibitor AZ20 Deposited 2020-07-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1522–1656（135 aa）	Not recorded	VCD 4-{4-[(3R)-3-methylmorpholin-4-yl]-6-[1-(methylsulfonyl)cyclopropyl]pyrimidin-2-yl}-1H-indole × 1 EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.01 M Co(II) chloride, 0.1 M Sodium acetate trihydrate (pH 4.6), 1 M 1,6-Hexanediol	Resolution 1.60 Å R-free 0.195
7JJH Crystal structure of the unliganded tandem bromodomain (BD1, BD2) of human TAF1 Deposited 2020-07-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1373–1635（263 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.8 M Succinic Acid, pH 7.0	Resolution 2.10 Å R-free 0.220
7JSP Crystal structure of the second bromodomain (BD2) of human TAF1 bound to ATR kinase inhibitor AZD6738 Deposited 2020-08-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1522–1656（135 aa）	Not recorded	VJM 4-(4-{1-[(R)-amino(hydroxy)methyl-lambda~4~-sulfanyl]cyclopropyl}-6-[(3R)-3-methylmorpholin-4-yl]pyrimidin-2-yl)-1H-pyrrolo[2,3-b]pyridine × 1 EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.01 M Co(II) chloride, 0.1 M Sodium acetate trihydrate (pH 4.6), 1 M 1,6-Hexanediol	Resolution 1.70 Å R-free 0.205
7JTC Crystal structure of the second bromodomain (BD2) of human TAF1 bound to ZS1-322 Deposited 2020-08-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1522–1656（135 aa）	Not recorded	VK1 1-{6-[(3R)-3-methylmorpholin-4-yl]-2-(methylsulfanyl)pyrimidin-4-yl}cyclopropane-1-sulfonimidoamide × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.01 M Co(II) chloride, 0.1 M Sodium acetate trihydrate (pH 4.6), 1 M 1,6-Hexanediol	Resolution 2.05 Å R-free 0.232
7K03 Crystal structure of the tandem bromodomain (BD1 and BD2) of human TAF1 bound to ATR kinase inhibitor AZD6738 Deposited 2020-09-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1373–1635（263 aa） Fragment：Tandem bromodomains, residues 1373-1635	Not recorded	VJM 4-(4-{1-[(R)-amino(hydroxy)methyl-lambda~4~-sulfanyl]cyclopropyl}-6-[(3R)-3-methylmorpholin-4-yl]pyrimidin-2-yl)-1H-pyrrolo[2,3-b]pyridine × 1 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Magnesium acetate tetrahydrate, 0.1 M Sodium cacodylate trihydrate, 20% Polyethylene glycol 8,000	Resolution 1.60 Å R-free 0.180
7K0D Crystal structure of the tandem bromodomain (BD1, BD2) of human TAF1 bound to mTORC1/2 inhibitor AZD3147 Deposited 2020-09-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1373–1635（263 aa） Fragment：TANDEM BROMODOMAINS, RESIDUES 1373-1635	Not recorded	VQS N-(4-{4-[1-(cyclopropylsulfonyl)cyclopropyl]-6-[(3S)-3-methylmorpholin-4-yl]pyrimidin-2-yl}phenyl)-N'-(2-hydroxyethyl)thiourea × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Ammonium sulfate, 0.1 M MES monohydrate, 30% Polyethylene glycol monomethyl ether 5,000	Resolution 2.20 Å R-free 0.249
7K0U Crystal structure of the second bromodomain (BD2) of human TAF1 bound to PLK1 kinase inhibitor BI2536 Deposited 2020-09-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1501–1635（135 aa） Chain B 1501–1635（135 aa）	Not recorded	R78 4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M HEPES (pH 7.5), 10% PEG 8,000, 8% Ethylene glycol	Resolution 2.52 Å R-free 0.245
7K1P Crystal structure of the second bromodomain (BD2) of human TAF1 bound to bromosporine Deposited 2020-09-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1501–1635（135 aa）	Not recorded	BMF Bromosporine × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M HEPES (pH 7.5), 10% PEG 8,000, 8% Ethylene glycol	Resolution 2.45 Å R-free 0.220
7K27 Crystal structure of the tandem bromodomain (BD1, BD2) of human TAF1 bound to ATR inhibitor AZ20 Deposited 2020-09-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1373–1635（263 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 4 VCD 4-{4-[(3R)-3-methylmorpholin-4-yl]-6-[1-(methylsulfonyl)cyclopropyl]pyrimidin-2-yl}-1H-indole × 1 DMS DIMETHYL SULFOXIDE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Magnesium chloride hexahydrate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350	Resolution 1.50 Å R-free 0.175
7K3O Crystal structure of the unliganded second bromodomain (BD2) of human TAF1 Deposited 2020-09-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1501–1635（135 aa） Chain B 1501–1635（135 aa）	Not recorded	SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Potassium sodium tartrate tetrahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 2.0 M Ammonium sulfate, 25% v/v Ethylene glycol	Resolution 1.70 Å R-free 0.202
7K42 Crystal structure of the second bromodomain (BD2) of human TAF1 bound to dioxane Deposited 2020-09-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1501–1635（135 aa） Chain B 1501–1635（135 aa）	Not recorded	SO4 SULFATE ION × 2 DIO 1,4-DIETHYLENE DIOXIDE × 2 EDO 1,2-ETHANEDIOL × 22	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Potassium sodium tartrate tetrahydrate, 0.1 M Sodium acetate tribasic dihydrate pH 5.6, 2.0 M Ammonium sulfate, 25% v/v Ethylene glycol	Resolution 1.70 Å R-free 0.190
7K6F Crystal structure of the tandem bromodomain (BD1, BD2) of human TAF1 in complex with MES (2-(N-morpholino)ethanesulfonic acid) Deposited 2020-09-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1373–1635（263 aa）	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 EDO 1,2-ETHANEDIOL × 3 ACT ACETATE ION × 2 FMT FORMIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Carboxylic acid (0.02M Sodium formate; 0.02M Ammonium acetate; 0.02M Sodium citrate tribasic dihydrate; 0.02M Potassium sodium tartrate tetrahydrate; 0.02M Sodium oxamate), 0.1M Buffer system 1 pH 6.5 (Imidazole; MES monohydrate), 30% precipitant mix 3 (20% v/v Glycerol; 10% w/v PEG 4000)	Resolution 1.86 Å R-free 0.203
7L6X Crystal structure of the tandem bromodomain (BD1, BD2) of human TAF1 bound to GNE-371 Deposited 2020-12-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1373–1635（263 aa）	Not recorded	G9V 6-(but-3-en-1-yl)-4-[1-methyl-6-(morpholine-4-carbonyl)-1H-benzimidazol-4-yl]-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Amino acids, 0.1M Buffer system 1 pH 6.5, 30% v/v precipitant mix 3 (morpheus screen 2-39)	Resolution 2.75 Å R-free 0.250
7LB0 Crystal structure of the tandem bromodomain (BD1, BD2) of human TAF1 bound to ZS1-295 Deposited 2021-01-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1373–1635（263 aa）	Not recorded	XXV 1-{6-[(3R)-3-methylmorpholin-4-yl]-2-(1H-pyrrolo[2,3-b]pyridin-4-yl)pyrimidin-4-yl}cyclopropane-1-sulfonamide × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M MgCl2, 0.1 M Bis-Tris pH 6.5, 25% PEG 3350	Resolution 2.33 Å R-free 0.220
7LB1 Crystal structure of the tandem bromodomain (BD1, BD2) of human TAF1 bound to ZS1-585 Deposited 2021-01-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1373–1635（263 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 18 PEG DI(HYDROXYETHYL)ETHER × 1 XWV 5-{4-[(3R)-3-methylmorpholin-4-yl]-6-[1-(S-methylsulfonimidoyl)cyclopropyl]pyrimidin-2-yl}isoquinoline × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.15 M MgCl2, 0.1 M Bis-Tris pH 5.5, 15% PEG 3350	Resolution 1.35 Å R-free 0.179
7LB2 Crystal structure of the tandem bromodomain (BD1, BD2) of human TAF1 bound to ZS1-589 Deposited 2021-01-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1373–1635（263 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 8 HEZ HEXANE-1,6-DIOL × 1 XWY (3R)-3-methyl-4-{6-[1-(S-methylsulfonimidoyl)cyclopropyl]-2-(naphthalen-1-yl)pyrimidin-4-yl}morpholine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.15 M MgCl2, 0.1 M Bis-Tris pH 5.5, 15% PEG 3350	Resolution 1.70 Å R-free 0.200
7LB3 Crystal structure of the second bromodomain (BD2) of human TAF1 bound to ZS1-580 Deposited 2021-01-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1501–1635（135 aa） Fragment：second bromodomain	Not recorded	XXS 4-{4-[(3R)-3-methylmorpholin-4-yl]-6-[1-(S-methylsulfonimidoyl)cyclopropyl]pyrimidin-2-yl}-1H-indazole × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.15 M MgCl2, 0.1 M Bis-Tris pH 5.5, 15% PEG 3350	Resolution 1.90 Å R-free 0.208
7N42 Crystal structure of the tandem bromodomain of human TAF1 (TAF1-T) bound to ZS1-681 Deposited 2021-06-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1373–1635（263 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 7 06M 6-(but-3-en-1-yl)-4-[6-{1-[(R)-S-methanesulfonimidoyl]cyclopropyl}-2-(1H-pyrrolo[2,3-b]pyridin-4-yl)pyrimidin-4-yl]-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.15 M MgCl2, 0.1 M Bis-Tris pH 5.5, 15% PEG 3,350	Resolution 1.90 Å R-free 0.204
7P4S BROMODOMAIN OF HUMAN TAF1 (2) WITH naphthyridinone compound Deposited 2021-07-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1501–1635（135 aa）	Not recorded	5LV 8-[[1-(3-azanylpropyl)piperidin-4-yl]amino]-5-[5-(hydroxymethyl)pyridin-3-yl]-3-methyl-1~{H}-1,7-naphthyridin-2-one × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；278 K；30% w/v EDO_P8K, 0.1M Morpheus buffer 2 and 10% morpheus alcohols	Resolution 2.17 Å R-free 0.274
7T2I Crystal structure of the tandem bromodomain (BD1, BD2) of human TAF1 bound to ZS1-588 Deposited 2021-12-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1373–1635（263 aa）	Not recorded	DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 3 E9F 4-(6-{1-[(R)-S-methanesulfonimidoyl]cyclopropyl}-2-[(3R)-3-methylmorpholin-4-yl]pyrimidin-4-yl)-1H-pyrrolo[2,3-b]pyridine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.15 M MgCl2, 0.1 M Bis-Tris pH 5.5, 15% PEG 3,350	Resolution 1.89 Å R-free 0.199
7T36 Crystal structure of the tandem bromodomain (BD1 and BD2) of human TAF1 bound to ZS1-322 Deposited 2021-12-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1373–1635（263 aa）	Not recorded	EIO (3R)-4-[6-{1-[diamino(hydroxy)-lambda~4~-sulfanyl]cyclopropyl}-2-(methylsulfanyl)pyrimidin-4-yl]-3-methylmorpholine × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.15 M MgCl2, 0.1 M Bis-Tris pH 5.5, 15% PEG 3,350	Resolution 1.65 Å R-free 0.203
8GXQ PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state Deposited 2022-09-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric	Chain DA 1–1872（1872 aa）	Not recorded	ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.04 Å
8GXS PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state Deposited 2022-09-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric	Chain DA 1–1872（1872 aa）	Not recorded	ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.16 Å
8WAK Structure of transcribing complex 2 (TC2), the initially transcribing complex with Pol II positioned 2nt downstream of TSS. Deposited 2023-09-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric	Chain A 1–1872（1872 aa）	Not recorded	ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.47 Å
8WAL Structure of transcribing complex 3 (TC3), the initially transcribing complex with Pol II positioned 3nt downstream of TSS. Deposited 2023-09-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric	Chain A 1–1872（1872 aa）	Not recorded	ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.52 Å
8WAN Structure of transcribing complex 4 (TC4), the initially transcribing complex with Pol II positioned 4nt downstream of TSS. Deposited 2023-09-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric	Chain A 1–1872（1872 aa）	Not recorded	ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.07 Å
8WAO Structure of transcribing complex 5 (TC5), the initially transcribing complex with Pol II positioned 5nt downstream of TSS. Deposited 2023-09-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric	Chain A 1–1872（1872 aa）	Not recorded	ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.40 Å
8WAP Structure of transcribing complex 6 (TC6), the initially transcribing complex with Pol II positioned 6nt downstream of TSS. Deposited 2023-09-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric	Chain A 1–1872（1872 aa）	Not recorded	ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.85 Å
8WAQ Structure of transcribing complex 7 (TC7), the initially transcribing complex with Pol II positioned 7nt downstream of TSS. Deposited 2023-09-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric	Chain A 1–1872（1872 aa）	Not recorded	ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.29 Å
8WAR Structure of transcribing complex 8 (TC8), the initially transcribing complex with Pol II positioned 8nt downstream of TSS. Deposited 2023-09-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric	Chain A 1–1872（1872 aa）	Not recorded	ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.20 Å
8WAS Structure of transcribing complex 9 (TC9), the initially transcribing complex with Pol II positioned 9nt downstream of TSS. Deposited 2023-09-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric	Chain A 1–1872（1872 aa）	Not recorded	ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.13 Å

62 other PDB entries and 65 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TAF1_HUMAN
Isoform	P21675-12
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–138； UniProt 1521–1656

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	6p39
Deposition date deposition_date	2019-05-23
Structure title title	Crystal Structure Analysis of TAF1 Bromodomain
Keywords keywords	kinase, bromodomain, inhibitor, TRANSCRIPTION, TRANSFERASE; TRANSFERASE
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	17.01 Å
Radius of gyration Rg (electron density) rg_electron	16.18 Å
Forward intensity I(0) i0	4443160.00
Molecular weight molecular_weight	15312.0 kDa
Excluded volume excluded_volume	19217 Å³
Envelope volume envelope_volume	22101 Å³
Hydration-shell volume shell_volume	12296 Å³
Envelope diameter envelope_diameter	60.4 Å
Shell Rg shell_rg	21.31 Å
Envelope Rg envelope_rg	16.75 Å
Shape Rg shape_rg	16.19 Å
Total Rg total_rg	17.11 Å
Total atoms total_atoms	1080
Residues n_residues	128
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	61.3 Å
Rg (real space) rg_real	17.09 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	4.4430e+06
I(0) uncertainty (real space) i0_real_error	5.8660e+04
Rg (reciprocal space) rg_reciprocal	17.08 Å
I(0) (reciprocal space) i0_reciprocal	4443000.0000
Solution quality estimate total_estimate	0.8197
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.7 Å
Skewness Skewness skewness	0.512
Kurtosis Kurtosis kurtosis	-0.097
Angular range angular_range	— – 0.4700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	959800.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.610; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.839; Smooth: 0.982

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d6p39a_
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.2 — Bromodomain
Family Family family	a.29.2.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	6p39A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

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8. Citations (1)

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Unit-cell length a length_a	96.600 Å
Unit-cell length b length_b	96.600 Å
Unit-cell length c length_c	91.130 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	6

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

Resolution resolution	2.941 Å
Low-resolution limit resolution_low	42.676 Å
R factor r_factor	0.1936
R_work r_work	0.1926
R_free r_free	0.2123

Description description	Transcription initiation factor TFIID subunit 1
Molecular weight formula_weight	15997.9 kDa
EC 编号 ec_number	2.3.1.48,2.7.11.1
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1080

Crystal Structure Analysis of TAF1 Bromodomain

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

Transcription initiation factor TFIID subunit 1

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	;3-methoxy-4-{[(6aR)-5-methyl-6-oxo-6,6a,7,8,9,10-hexahydro-5H-dipyrido[1,2-a:3',2'-e]pyrazin-2-yl]amino}-N-(1-methylpiperidin-4-yl)benzamide ;
Molecular weight formula_weight	478.6 kDa
Source method src_method	syn
Copy count entity_count	1

fit	/app/data/saxs_computation/p3/6p39/6p39.fit
pddf	/app/data/pr_computation/p3/6p39/6p39.pr.out
profile	/app/data/saxs_computation/p3/6p39/6p39.dat