1ytb

CRYSTAL STRUCTURE OF A YEAST TBP/TATA-BOX COMPLEX

Method: X-RAY DIFFRACTION D_max: 96.8 Å Quality: GOOD

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

PROTEIN (TATA BINDING PROTEIN (TBP))

Saccharomyces cerevisiae

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–DNA Monomer Protein × 1 DNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain A； UniProt 60–239	Not recorded	DNA (29MER) × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 295.00K	Resolution 1.80 Å R-free 0.261
2	Protein–DNA Monomer Protein × 1 DNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain B； UniProt 60–239	Not recorded	DNA (29MER) × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 295.00K	Resolution 1.80 Å R-free 0.261

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 1YTB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1NGM Crystal structure of a yeast Brf1-TBP-DNA ternary complex Deposited 2002-12-17	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 60–239（180 aa） Fragment：C-terminal core domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；MES, NaCl, BME, glycerol, MgCl2, PEG2000MME, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.95 Å R-free 0.308
1NGM Crystal structure of a yeast Brf1-TBP-DNA ternary complex Deposited 2002-12-17	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain E 60–239（180 aa） Fragment：C-terminal core domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；MES, NaCl, BME, glycerol, MgCl2, PEG2000MME, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.95 Å R-free 0.308
1NGM Crystal structure of a yeast Brf1-TBP-DNA ternary complex Deposited 2002-12-17	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain I 60–239（180 aa） Fragment：C-terminal core domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；MES, NaCl, BME, glycerol, MgCl2, PEG2000MME, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.95 Å R-free 0.308
1NGM Crystal structure of a yeast Brf1-TBP-DNA ternary complex Deposited 2002-12-17	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain M 60–239（180 aa） Fragment：C-terminal core domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；MES, NaCl, BME, glycerol, MgCl2, PEG2000MME, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.95 Å R-free 0.308
1NH2 Crystal structure of a yeast TFIIA/TBP/DNA complex Deposited 2002-12-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain A 60–239（180 aa） Fragment：C-TERMINAL 180 RESIDUES	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å R-free 0.226
1RM1 Structure of a Yeast TFIIA/TBP/TATA-box DNA Complex Deposited 2003-11-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain A 1–239（239 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；PEG 4000, ammonium citrate, MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.50 Å R-free 0.252
1TBA SOLUTION STRUCTURE OF A TBP-TAFII230 COMPLEX: PROTEIN MIMICRY OF THE MINOR GROOVE SURFACE OF THE TATA BOX UNWOUND BY TBP, NMR, 25 STRUCTURES Deposited 1998-08-16	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 60–239（180 aa） Fragment：CORE DOMAIN RESIDUES 60-249	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K	Resolution not provided
1TBP CRYSTAL STRUCTURE OF YEAST TATA-BINDING PROTEIN AND MODEL FOR INTERACTION WITH DNA Deposited 1993-08-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 61–239（179 aa） Chain B 61–239（179 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å
1YTF YEAST TFIIA/TBP/DNA COMPLEX Deposited 1996-04-05	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain A 60–239（180 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.297
4B0A The high-resolution structure of yTBP-yTAF1 identifies conserved and competing interaction surfaces in transcriptional activation Deposited 2012-06-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 61–240（180 aa） Fragment：TAF1 RESIDUES 8-71, LINKER, TBP RESIDUE 61-240	Mutation：YES	CA CALCIUM ION × 3 GOL GLYCEROL × 6 CL CHLORIDE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.97 Å R-free 0.223
4V1N Architecture of the RNA polymerase II-Mediator core transcription initiation complex Deposited 2014-09-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric	Chain O 61–240（180 aa） Fragment：RESIDUES 61-240	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer 25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT；pH 7.5；25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT cryo-EM vitrification conditions Cryogen ETHANE；GRIDS WERE GLOW- DISCHARGED FOR 20 S BEFORE DEPOSITION OF 4 MICROLITERS SAMPLE AND INCUBATED FOR 30 S. GRIDS WERE WASHED TWICE WITH 4 MICROLITERS DISTILLED WATER, BLOTTED, AND VITRIFIED BY PLUNGING INTO LIQUID ETHANE WITH A MANUAL PLUNGER.	Resolution 7.80 Å
4V1O Architecture of the RNA polymerase II-Mediator core transcription initiation complex Deposited 2014-09-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric	Chain O 61–240（180 aa） Fragment：RESIDUES 61-240	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer 25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT；pH 7.5；25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT cryo-EM vitrification conditions Cryogen ETHANE；GRIDS WERE GLOW- DISCHARGED FOR 20 S BEFORE DEPOSITION OF 4 MICROLITERS SAMPLE AND INCUBATED FOR 30 S. GRIDS WERE WASHED TWICE WITH 4 MICROLITERS DISTILLED WATER, BLOTTED, AND VITRIFIED BY PLUNGING INTO LIQUID ETHANE WITH A MANUAL PLUNGER.	Resolution 9.70 Å
5FMF the P-lobe of RNA polymerase II pre-initiation complex Deposited 2015-11-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric	Chain Q 61–240（180 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 9	ELECTRON MICROSCOPY cryo-EM buffer 20 MM HEPES (PH7.6), 5 MM DTT, 2 MM MG(OAC)2,AND 40 MM KOAC；pH 7.6；20 MM HEPES (PH7.6), 5 MM DTT, 2 MM MG(OAC)2,AND 40 MM KOAC cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 120, INSTRUMENT- FEI VITROBOT MARK III,	Resolution 6.00 Å
5FYW Transcription initiation complex structures elucidate DNA opening (OC) Deposited 2016-03-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric	Chain O 1–240（240 aa）	Not recorded	ZN ZINC ION × 10 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer 25 MM HEPES-KOH PH 7.5, 150 MM POTASSIUM ACETATE, 2 MM MGCL2, 5 MM DTT；pH 7.5；25 MM HEPES-KOH PH 7.5, 150 MM POTASSIUM ACETATE, 2 MM MGCL2, 5 MM DTT cryo-EM vitrification conditions Cryogen ETHANE；CRYOGEN - ETHANE. INSTRUMENT - FEI VITROBOT MARK IV. QUANTIFOIL R 3.5- 1 HOLEY CARBON GRIDS WERE GLOW-DISCHARGED BEFORE DEPOSITION OF 4.5 MICROLITERS OF SAMPLE. GRIDS WERE THEN BLOTTED FOR 8.5 S AND PLUNGE- FROZEN IN LIQUID ETHANE.	Resolution 4.35 Å
5FZ5 Transcription initiation complex structures elucidate DNA opening (CC) Deposited 2016-03-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric	Chain O 1–240（240 aa）	Not recorded	ZN ZINC ION × 10 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer 25 MM HEPES-KOH PH 7.5, 150 MM POTASSIUM ACETATE, 2 MM MGCL2, 5 MM DTT；pH 7.5；25 MM HEPES-KOH PH 7.5, 150 MM POTASSIUM ACETATE, 2 MM MGCL2, 5 MM DTT cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE	Resolution 8.80 Å
5OQJ STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH Deposited 2017-08-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric	Chain O 1–240（240 aa）	Not recorded	ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；GRIDS WERE BLOTTED FOR 8 S AND PLUNGE-FROZEN IN LIQUID ETHANE.	Resolution 4.70 Å
5OQM STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH AND CORE MEDIATOR Deposited 2017-08-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric	Chain O 1–240（240 aa）	Not recorded	ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 8 s and plunge-frozen in liquid ethane.	Resolution 5.80 Å
5SVA Mediator-RNA Polymerase II Pre-Initiation Complex Deposited 2016-08-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric	Chain j 1–240（240 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 15.30 Å
6CNB Yeast RNA polymerase III initial transcribing complex Deposited 2018-03-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 19 PDB declaration: 21-meric	Chain R 61–240（180 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
6CNC Yeast RNA polymerase III open complex Deposited 2018-03-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 19 PDB declaration: 21-meric	Chain R 61–240（180 aa）	Mutation：C438S	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
6CND Yeast RNA polymerase III natural open complex (nOC) Deposited 2018-03-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 19 PDB declaration: 21-meric	Chain R 61–240（180 aa）	Mutation：C438S	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
6CNF Yeast RNA polymerase III elongation complex Deposited 2018-03-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 19 PDB declaration: 21-meric	Chain R 61–240（180 aa）	Mutation：C438S	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å
6E16 Ternary structure of c-Myc-TBP-TAF1 Deposited 2018-07-09	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 61–240（180 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；291 K；20% (w/w) PEG8000, 0.2M ammonium sulfare, and 0.1M HEPES pH7.5	Resolution 2.40 Å R-free 0.220
6E24 Ternary structure of c-Myc-TBP-TAF1 Deposited 2018-07-10	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 61–240（180 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；16% W/V PEG3350 0.05M CITRIC ACID 0.05M BIS-TRIS PROPANE pH5.0	Resolution 3.00 Å R-free 0.224
6EU0 RNA Polymerase III open pre-initiation complex (OC-PIC) Deposited 2017-10-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric	Chain Y 1–240（240 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
6F40 RNA Polymerase III open complex Deposited 2017-11-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric	Chain U 1–240（240 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
6F41 RNA Polymerase III initially transcribing complex Deposited 2017-11-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric	Chain U 1–240（240 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
6F42 RNA Polymerase III closed complex CC1. Deposited 2017-11-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric	Chain U 1–240（240 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.50 Å
6F44 RNA Polymerase III closed complex CC2. Deposited 2017-11-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric	Chain U 1–240（240 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
6GYK Structure of a yeast closed complex (core CC1) Deposited 2018-06-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric	Chain O 1–240（240 aa）	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.10 Å
6GYL Structure of a yeast closed complex with distorted DNA (core CCdist) Deposited 2018-06-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric	Chain O 1–240（240 aa）	Not recorded	ZN ZINC ION × 10 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
6GYM Structure of a yeast closed complex with distorted DNA (CCdist) Deposited 2018-06-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric	Chain O 1–240（240 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.70 Å
7ML0 RNA polymerase II pre-initiation complex (PIC1) Deposited 2021-04-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric	Chain O 1–240（240 aa）	Not recorded	ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
7ML1 RNA polymerase II pre-initiation complex (PIC2) Deposited 2021-04-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain O 1–240（240 aa）	Not recorded	ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7ML4 RNA polymerase II initially transcribing complex (ITC) Deposited 2021-04-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 28 PDB declaration: 31-meric	Chain O 1–240（240 aa）	Not recorded	ZN ZINC ION × 15 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7O4I Yeast RNA polymerase II transcription pre-initiation complex with initial transcription bubble Deposited 2021-04-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain O 1–240（240 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7O4J Yeast RNA polymerase II transcription pre-initiation complex (consensus) Deposited 2021-04-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain O 1–240（240 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
7O72 Yeast RNA polymerase II transcription pre-initiation complex with closed promoter DNA Deposited 2021-04-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain O 1–240（240 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7O73 Yeast RNA polymerase II transcription pre-initiation complex with closed distorted promoter DNA Deposited 2021-04-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain O 1–240（240 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7O75 Yeast RNA polymerase II transcription pre-initiation complex with open promoter DNA Deposited 2021-04-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain O 1–240（240 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7Q5B Cryo-EM structure of Ty3 retrotransposon targeting a TFIIIB-bound tRNA gene Deposited 2021-11-03	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: tridecameric	Chain Y 1–240（240 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.98 Å
7Z0O Structure of transcription factor UAF in complex with TBP and 35S rRNA promoter DNA Deposited 2022-02-23	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain H 1–240（240 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
7ZS9 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A) Deposited 2022-05-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain O 1–240（240 aa）	Not recorded	ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7ZSA Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B) Deposited 2022-05-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain O 1–240（240 aa）	Not recorded	ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7ZSB Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP, complex C Deposited 2022-05-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain O 1–240（240 aa）	Not recorded	ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.60 Å
8FFZ TFIIIA-TFIIIC-Brf1-TBP complex bound to 5S rRNA gene Deposited 2022-12-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: decameric	Chain H 61–240（180 aa）	Not recorded	ZN ZINC ION × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
8H5B The cryo-EM structure of nuclear transport receptor Kap114p complex with yeast TATA-box binding protein Deposited 2022-10-12	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 61–240（180 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.03 Å
8UMH Consensus map of PICdeltaTFIIK form2 Deposited 2023-10-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain O 1–240（240 aa）	Not recorded	ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
8UMI consensus map of PICdeltaTFIIK form1 Deposited 2023-10-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain O 1–240（240 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
8UOQ Composite map of PIC_delta_TFIIK form2 Deposited 2023-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain O 1–240（240 aa）	Not recorded	ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
8UOT Composite map of PICdeltaTFIIK form1 Deposited 2023-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain O 1–240（240 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

48 other PDB entries and 51 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TBP_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–180； UniProt 60–239 Author chain B； PDBConstruct 1–180； UniProt 60–239

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	1ytb
Deposition date deposition_date	1994-09-28
Structure title title	CRYSTAL STRUCTURE OF A YEAST TBP/TATA-BOX COMPLEX
Keywords keywords	PROTEIN-DNA COMPLEX, TRANSCRIPTION-DNA COMPLEX; TRANSCRIPTION/DNA
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	26.93 Å
Radius of gyration Rg (electron density) rg_electron	26.76 Å
Forward intensity I(0) i0	73025600.00
Molecular weight molecular_weight	58204.0 kDa
Excluded volume excluded_volume	69128 Å³
Envelope volume envelope_volume	93103 Å³
Hydration-shell volume shell_volume	29480 Å³
Envelope diameter envelope_diameter	98.1 Å
Shell Rg shell_rg	33.64 Å
Envelope Rg envelope_rg	26.22 Å
Shape Rg shape_rg	26.77 Å
Total Rg total_rg	27.37 Å
Total atoms total_atoms	4026
Residues n_residues	418
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	96.8 Å
Rg (real space) rg_real	26.85 Å
Rg uncertainty (real space) rg_real_error	0.97 Å
I(0) (real space) i0_real	7.3030e+07
I(0) uncertainty (real space) i0_real_error	1.2020e+06
Rg (reciprocal space) rg_reciprocal	26.88 Å
I(0) (reciprocal space) i0_reciprocal	73030000.0000
Solution quality estimate total_estimate	0.7694
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	36.1 Å
Skewness Skewness skewness	0.245
Kurtosis Kurtosis kurtosis	-0.251
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12490000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.685; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.944; Smooth: 0.000

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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	DNA (29MER)
Molecular weight formula_weight	8987.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,D
Atom count atom_count	4539

GTATATAAAACGGGTGGCGTTTTATATAC

Entity 2 Entity 2 polymer

Description description	PROTEIN (TATA BINDING PROTEIN (TBP))
Molecular weight formula_weight	20120.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SGIVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVVTGAKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHGTFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEFRKM

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	513

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1ytba1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.129 — TBP-like
Superfamily Superfamily superfamily	d.129.1 — TATA-box binding protein-like
Family Family family	d.129.1.1 — TATA-box binding protein (TBP), C-terminal domain

Domain ID domain_id	d1ytba2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.129 — TBP-like
Superfamily Superfamily superfamily	d.129.1 — TATA-box binding protein-like
Family Family family	d.129.1.1 — TATA-box binding protein (TBP), C-terminal domain

Domain ID domain_id	d1ytbb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.129 — TBP-like
Superfamily Superfamily superfamily	d.129.1 — TATA-box binding protein-like
Family Family family	d.129.1.1 — TATA-box binding protein (TBP), C-terminal domain

Domain ID domain_id	d1ytbb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.129 — TBP-like
Superfamily Superfamily superfamily	d.129.1 — TATA-box binding protein-like
Family Family family	d.129.1.1 — TATA-box binding protein (TBP), C-terminal domain

CATH v4.4 (4 domains)

Domain ID domain_id	1ytbA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	10 — TATA-Binding Protein

Domain ID domain_id	1ytbA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	10 — TATA-Binding Protein

Domain ID domain_id	1ytbB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	10 — TATA-Binding Protein

Domain ID domain_id	1ytbB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	10 — TATA-Binding Protein

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8. Citations (1)

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Unit-cell length a length_a	100.770 Å
Unit-cell length b length_b	100.770 Å
Unit-cell length c length_c	66.500 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.2010
R_work r_work	0.2010
R_free r_free	0.2610

fit	/app/data/saxs_computation/yt/1ytb/1ytb.fit
pddf	/app/data/pr_computation/yt/1ytb/1ytb.pr.out
profile	/app/data/saxs_computation/yt/1ytb/1ytb.dat

CRYSTAL STRUCTURE OF A YEAST TBP/TATA-BOX COMPLEX

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

PROTEIN (TATA BINDING PROTEIN (TBP))

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)