8h5b

The cryo-EM structure of nuclear transport receptor Kap114p complex with yeast TATA-box binding protein

Method: ELECTRON MICROSCOPY D_max: 113.6 Å Quality: EXCELLENT

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

Importin subunit beta-5

Saccharomyces cerevisiae S288C

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 1–1004	Not recorded	TATA-box-binding protein × 1 （P13393）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.03 Å

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 8H5B	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6AHO Crystal structure of Kap114p Deposited 2018-08-20	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1004（1004 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.43 M citric acid, 0.057 M BIS TRIS propane (pH 5.8), 17% PEG3350, 0.01 M Ethylenediaminetetraacetic acid disodium salt dihydrate, and 3% v/v ethanol	Resolution 2.50 Å R-free 0.263
8F0X Cryo-EM structure of Kap114 bound to H2A-H2B Deposited 2022-11-04	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1004（1004 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Tris pH 7.5, 300 mM NaCl, 2 mM MgCl2, 1 mM TCEP, and 0.1% NP-40 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.21 Å
8F19 Cryo-EM structure of Kap114 bound to Gsp1 (RanGTP) Deposited 2022-11-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–1004（1004 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Tris pH 7.5, 300 mM NaCl, 2 mM MgCl2, 1 mM TCEP, and 0.1% NP-40 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.49 Å
8F1E Cryo-EM structure of Kap114 bound to Gsp1 (RanGTP) and H2A-H2B Deposited 2022-11-04	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 1–1004（1004 aa）	Not recorded	MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.28 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IMB5_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1004； UniProt 1–1004

TATA-box-binding protein

Saccharomyces cerevisiae S288C

UniProt P13393

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 61–240	Not recorded	Importin subunit beta-5 × 1 （P53067）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.03 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8H5B	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 method 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 method 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 method 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 method 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 method 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 method 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 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 method 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
1YTB CRYSTAL STRUCTURE OF A YEAST TBP/TATA-BOX COMPLEX Deposited 1994-09-28	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 60–239（180 aa）	Not recorded	No recorded non-water small molecule	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
1YTB CRYSTAL STRUCTURE OF A YEAST TBP/TATA-BOX COMPLEX Deposited 1994-09-28	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 60–239（180 aa）	Not recorded	No recorded non-water small molecule	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
1YTF YEAST TFIIA/TBP/DNA COMPLEX Deposited 1996-04-05	Different construct Different oligomeric state Different experimental method 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 method 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 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 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 oligomeric state Different ligand/ion 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 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 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 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 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 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 oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 oligomeric state Different ligand/ion 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
8UMH Consensus map of PICdeltaTFIIK form2 Deposited 2023-10-17	Different construct Different oligomeric state Different ligand/ion 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 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 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 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 52 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 B； PDBConstruct 1–180； UniProt 61–240

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	8h5b
Deposition date deposition_date	2022-10-12
最后修订 last_revision	2023-09-20
Structure title title	The cryo-EM structure of nuclear transport receptor Kap114p complex with yeast TATA-box binding protein
Keywords keywords	nuclear transport receptor Kap114p, yeast TATA-box binding protein, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	36.77 Å
Radius of gyration Rg (electron density) rg_electron	36.14 Å
Forward intensity I(0) i0	208841000.00
Molecular weight molecular_weight	121760.0 kDa
Excluded volume excluded_volume	154900 Å³
Envelope volume envelope_volume	211010 Å³
Hydration-shell volume shell_volume	49008 Å³
Envelope diameter envelope_diameter	111.7 Å
Shell Rg shell_rg	42.43 Å
Envelope Rg envelope_rg	35.15 Å
Shape Rg shape_rg	36.14 Å
Total Rg total_rg	36.60 Å
Total atoms total_atoms	8570
Residues n_residues	1075
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	113.6 Å
Rg (real space) rg_real	36.62 Å
Rg uncertainty (real space) rg_real_error	0.83 Å
I(0) (real space) i0_real	2.0880e+08
I(0) uncertainty (real space) i0_real_error	3.3920e+06
Rg (reciprocal space) rg_reciprocal	36.72 Å
I(0) (reciprocal space) i0_reciprocal	208900000.0000
Solution quality estimate total_estimate	0.9135
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	44.9 Å
Skewness Skewness skewness	0.100
Kurtosis Kurtosis kurtosis	-0.704
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	26420000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.970; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.959

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Importin subunit beta-5
Molecular weight formula_weight	114019.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	8570

MDINELIIGAQSADKHTREVAETQLLQWCDSDASQVFKALANVALQHEASLESRQFALLSLRKLITMYWSPGFESYRSTSNVEIDVKDFIREVLLKLCLNDNENTKIKNGASYCIVQISAVDFPDQWPQLLTVIYDAISHQHSLNAMSLLNEIYDDVVSEEMFFEGGIGLATMEIVFKVLNTETSTLIAKIAALKLLKACLLQMSSHNEYDEASRKSFVSQCLATSLQILGQLLTLNFGNVDVISQLKFKSIIYENLVFIKNDFSRKHFSSELQKQFKIMAIQDLENVTHINANVETTESEPLLETVHDCSIYIVEFLTSVCTLQFSVEEMNKIITSLTILCQLSSETREIWTSDFNTFVSKETGLAASYNVRDQANEFFTSLPNPQLSLIFKVVSNDIEHSTCNYSTLESLLYLLQCILLNDDEITGENIDQSLQILIKTLENILVSQEIPELILARAILTIPRVLDKFIDALPDIKPLTSAFLAKSLNLALKSDKELIKSATLIAFTYYCYFAELDSVLGPEVCSETQEKVIRIINQVSSDAEEDTNGALMEVLSQVISYNPKEPHSRKEILQAEFHLVFTISSEDPANVQVVVQSQECLEKLLDNINMDNYKNYIELCLPSFINVLDSNNANNYRYSPLLSLVLEFITVFLKKKPNDGFLPDEINQYLFEPLAKVLAFSTEDETLQLATEAFSYLIFNTDTRAMEPRLMDIMKVLERLLSLEVSDSAAMNVGPLVVAIFTRFSKEIQPLIGRILEAVVVRLIKTQNISTEQNLLSVLCFLTCNDPKQTVDFLSSFQIDNTDALTLVMRKWIEAFEVIRGEKRIKENIVALSNLFFLNDKRLQKVVVNGNLIPYEGDLIITRSMAKKMPDRYVQVPLYTKIIKLFVSELSFQSKQPNPEQLITSDIKQEVVNANKDDDNDDWEDVDDVLDYDKLKEYIDDDVDEEADDDSDDITGLMDVKESVVQLLVRFFKEVASKDVSGFHCIYETLSDSERKVLSEALL

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288C
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	TATA-box-binding protein
Molecular weight formula_weight	20120.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SGIVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVVTGAKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHGTFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEFRKM

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288C
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

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8. Citations (1)

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Resolution resolution	4.03 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	212899

fit	/app/data/saxs_computation/h5/8h5b/8h5b.fit
pddf	/app/data/pr_computation/h5/8h5b/8h5b.pr.out
profile	/app/data/saxs_computation/h5/8h5b/8h5b.dat

The cryo-EM structure of nuclear transport receptor Kap114p complex with yeast TATA-box binding protein

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

Importin subunit beta-5

State in the Current Structure

Other States of the Same Protein in the Database

TATA-box-binding protein

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)