← Back to search
2phg

Model for VP16 binding to TFIIB

Method: SOLUTION NMR Dmax: 59.8 Å Quality: GOOD
▼

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

Transcription initiation factor IIB

Homo sapiens

UniProt Q00403

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 112–316 Fragment：c-terminal core domain Mutation：D111S Alpha trans-inducing protein × 1 （P06492） SOLUTION NMR NMR measurement conditions：pH 5.6；298 K；Ionic strength (raw mmCIF value) 100 mM；Pressure 1 NMR sample composition：0.2 mM VP16ad U-15N, 0-0.2 mM TFIIBc, 50 mM KCl, 50 mM phosphate buffer pH 5.6, 95% H2O, 5% D2O | 95% H2O/5% D2O Resolution not provided

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 2PHG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1C9B CRYSTAL STRUCTURE OF A HUMAN TBP CORE DOMAIN-HUMAN TFIIB CORE DOMAIN COMPLEX BOUND TO AN EXTENDED, MODIFIED ADENOVIRAL MAJOR LATE PROMOTER (ADMLP) Deposited 1999-08-01 Different construct Different mutation/modification 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 110–316（207 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；277 K；PEG 8000, TRIS.HCL, AMMONIUM ACETATE, MAGNESIUM CHLORIDE, POTASSIUM CHLORIDE, SODIUM CITRATE, DTT, GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.65 Å R-free 0.260
1C9B CRYSTAL STRUCTURE OF A HUMAN TBP CORE DOMAIN-HUMAN TFIIB CORE DOMAIN COMPLEX BOUND TO AN EXTENDED, MODIFIED ADENOVIRAL MAJOR LATE PROMOTER (ADMLP) Deposited 1999-08-01 Different construct Different mutation/modification 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 110–316（207 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；277 K；PEG 8000, TRIS.HCL, AMMONIUM ACETATE, MAGNESIUM CHLORIDE, POTASSIUM CHLORIDE, SODIUM CITRATE, DTT, GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.65 Å R-free 0.260
1C9B CRYSTAL STRUCTURE OF A HUMAN TBP CORE DOMAIN-HUMAN TFIIB CORE DOMAIN COMPLEX BOUND TO AN EXTENDED, MODIFIED ADENOVIRAL MAJOR LATE PROMOTER (ADMLP) Deposited 1999-08-01 Different construct Different mutation/modification 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 110–316（207 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；277 K；PEG 8000, TRIS.HCL, AMMONIUM ACETATE, MAGNESIUM CHLORIDE, POTASSIUM CHLORIDE, SODIUM CITRATE, DTT, GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.65 Å R-free 0.260
1C9B CRYSTAL STRUCTURE OF A HUMAN TBP CORE DOMAIN-HUMAN TFIIB CORE DOMAIN COMPLEX BOUND TO AN EXTENDED, MODIFIED ADENOVIRAL MAJOR LATE PROMOTER (ADMLP) Deposited 1999-08-01 Different construct Different mutation/modification 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 110–316（207 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；277 K；PEG 8000, TRIS.HCL, AMMONIUM ACETATE, MAGNESIUM CHLORIDE, POTASSIUM CHLORIDE, SODIUM CITRATE, DTT, GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.65 Å R-free 0.260
1C9B CRYSTAL STRUCTURE OF A HUMAN TBP CORE DOMAIN-HUMAN TFIIB CORE DOMAIN COMPLEX BOUND TO AN EXTENDED, MODIFIED ADENOVIRAL MAJOR LATE PROMOTER (ADMLP) Deposited 1999-08-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain Q 110–316（207 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；277 K；PEG 8000, TRIS.HCL, AMMONIUM ACETATE, MAGNESIUM CHLORIDE, POTASSIUM CHLORIDE, SODIUM CITRATE, DTT, GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.65 Å R-free 0.260
1DL6 SOLUTION STRUCTURE OF HUMAN TFIIB N-TERMINAL DOMAIN Deposited 1999-12-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–59（58 aa） Fragment：N-TERMINAL DOMAIN
Not recorded ZN ZINC ION × 1 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Pressure AMBIENT
NMR sample composition 3MM HTFIIB N-TERMINAL DOMAIN U-15N; 50MM PHOSPHATE; 90% H2O, 10% D2O
Resolution not provided
1RLY RDC-derived models of the zinc ribbon domain of human general transcription TFIIB (zinc bound structures) Deposited 2003-11-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–60（60 aa）
Not recorded ZN ZINC ION × 1 SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Pressure ambient
NMR sample composition 0.6mM TFIIB Uniform labeling with 15N: U-98% 15N, 20mM [2H4]-imidazole hydrochloride, 2.5mM ZnCl2, 5% glycerol, 20mM sodium sulfate at pH 6.5, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.6mM TFIIB Uniform labeling with 15N: U-98% 15N, 20mM [2H4]-imidazole hydrochloride, 2.5mM ZnCl2, 5% glycerol, 20mM sodium sulfate at pH 6.5, 12mg/mL of filamentous phage, Pf1, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
1RO4 RDC-derived models of the zinc ribbon domain of human general transcription factor TFIIB (zinc free structures) Deposited 2003-12-01 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–60（60 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Pressure ambient
NMR sample composition 0.6mM TFIIB Uniform labeling with 15N: U-98% 15N, 20mM [2H4]-imidazole hydrochloride, 5% glycerol and 20mM sodium sulfate at pH 6.5, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.6mM TFIIB Uniform labeling with 15N: U-98% 15N, 20mM [2H4]-imidazole hydrochloride, 5% glycerol and 20mM sodium sulfate at pH 6.5, 12mg/mL of filamentous phage, Pf1, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
1TFB NMR STUDIES OF HUMAN GENERAL TRANSCRIPTION FACTOR TFIIB: DYNAMICS AND INTERACTION WITH VP16 ACTIVATION DOMAIN, 20 STRUCTURES Deposited 1996-11-14 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 112–316（205 aa） Fragment：CONSTRUCT COMPRISES RESIDUES 1 - 3 AND 112 - 316 OF FULL LENGTH HUMAN TFIIB
Mutation：DEL(4 - 111) No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1VOL TFIIB (HUMAN CORE DOMAIN)/TBP (A.THALIANA)/TATA ELEMENT TERNARY COMPLEX Deposited 1996-04-29 Different construct Different mutation/modification 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 113–316（204 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å R-free 0.318
5IY6 Human holo-PIC in the closed state Deposited 2016-03-24 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 × 27 PDB declaration: 29-meric
Chain M 1–316（316 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.20 Å
5IY7 Human holo-PIC in the open state Deposited 2016-03-24 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 × 27 PDB declaration: 29-meric
Chain M 1–316（316 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 8.60 Å
5IY8 Human holo-PIC in the initial transcribing state Deposited 2016-03-24 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 × 27 PDB declaration: 29-meric
Chain M 1–316（316 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.90 Å
5IY9 Human holo-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain M 1–316（316 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 6.30 Å
5IYA Human core-PIC in the closed state Deposited 2016-03-24 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 × 21 PDB declaration: 23-meric
Chain M 1–316（316 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 5.40 Å
5IYB Human core-PIC in the open state Deposited 2016-03-24 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 × 21 PDB declaration: 23-meric
Chain M 1–316（316 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
5IYC Human core-PIC in the initial transcribing state Deposited 2016-03-24 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 × 21 PDB declaration: 23-meric
Chain M 1–316（316 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
5IYD Human core-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain M 1–316（316 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
5WH1 Apo form of the C-terminal region of human Transcription Factor IIB Deposited 2017-07-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 107–316（210 aa） Fragment：C-terminal residues 107-316
Not recorded SO4 SULFATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；100 mM sodium acetate trihydrate pH 4.5, 2 M ammonium sulfate
Resolution 3.39 Å R-free 0.214
5WH1 Apo form of the C-terminal region of human Transcription Factor IIB Deposited 2017-07-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 107–316（210 aa） Fragment：C-terminal residues 107-316
Not recorded SO4 SULFATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；100 mM sodium acetate trihydrate pH 4.5, 2 M ammonium sulfate
Resolution 3.39 Å R-free 0.214
5WH1 Apo form of the C-terminal region of human Transcription Factor IIB Deposited 2017-07-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 107–316（210 aa） Fragment：C-terminal residues 107-316
Not recorded SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；100 mM sodium acetate trihydrate pH 4.5, 2 M ammonium sulfate
Resolution 3.39 Å R-free 0.214
5WH1 Apo form of the C-terminal region of human Transcription Factor IIB Deposited 2017-07-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 107–316（210 aa） Fragment：C-terminal residues 107-316
Not recorded SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；100 mM sodium acetate trihydrate pH 4.5, 2 M ammonium sulfate
Resolution 3.39 Å R-free 0.214
6O9L Human holo-PIC in the closed state Deposited 2019-03-14 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 × 31 PDB declaration: 33-meric
Chain M 1–316（316 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
7EDX p53-bound TFIID-based core PIC on HDM2 promoter Deposited 2021-03-17 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 × 37 PDB declaration: 39-meric
Chain R 1–316（316 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 mutation/modification 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 R 1–316（316 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 mutation/modification 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 R 1–316（316 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 mutation/modification 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 R 1–316（316 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 mutation/modification 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 R 1–316（316 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 mutation/modification 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 R 1–316（316 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 mutation/modification 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 R 1–316（316 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
7ENA TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre-hPIC-MED) Deposited 2021-04-16 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 × 74 PDB declaration: 76-meric
Chain BA 1–316（316 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 mutation/modification 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 BA 1–316（316 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
7LBM Structure of the human Mediator-bound transcription pre-initiation complex Deposited 2021-01-08 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 × 54 PDB declaration: 56-meric
Chain O 1–316（316 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7NVR Human Mediator with RNA Polymerase II Pre-initiation complex Deposited 2021-03-15 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 × 56 PDB declaration: 58-meric
Chain M 1–316（316 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 18 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7NVS RNA polymerase II core pre-initiation complex with closed promoter DNA in proximal position Deposited 2021-03-16 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 × 20 PDB declaration: 22-meric
Chain M 1–316（316 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7NVT RNA polymerase II core pre-initiation complex with closed promoter DNA in distal position Deposited 2021-03-16 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 × 20 PDB declaration: 22-meric
Chain M 1–316（316 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7NVU RNA polymerase II core pre-initiation complex with open promoter DNA Deposited 2021-03-16 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 × 20 PDB declaration: 22-meric
Chain M 1–316（316 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7NVY RNA polymerase II pre-initiation complex with closed promoter DNA in proximal position Deposited 2021-03-16 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 × 30 PDB declaration: 32-meric
Chain M 1–316（316 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.30 Å
7NVZ RNA polymerase II pre-initiation complex with closed promoter DNA in distal position Deposited 2021-03-16 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 × 30 PDB declaration: 32-meric
Chain M 1–316（316 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
7NW0 RNA polymerase II pre-initiation complex with open promoter DNA Deposited 2021-03-16 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 × 30 PDB declaration: 32-meric
Chain M 1–316（316 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.60 Å
7ZWC Structure of SNAPc:TBP-TFIIA-TFIIB sub-complex bound to U5 snRNA promoter Deposited 2022-05-19 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 × 8 PDB declaration: decameric
Chain M 1–316（316 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7ZWD Structure of SNAPc containing Pol II pre-initiation complex bound to U5 snRNA promoter (CC) Deposited 2022-05-19 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 × 22 PDB declaration: 24-meric
Chain M 1–316（316 aa）
Not recorded ZN ZINC ION × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ZX7 Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (CC) Deposited 2022-05-20 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 × 22 PDB declaration: 24-meric
Chain M 1–316（316 aa）
Not recorded ZN ZINC ION × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ZX8 Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (OC) Deposited 2022-05-20 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 × 22 PDB declaration: 24-meric
Chain M 1–316（316 aa）
Not recorded ZN ZINC ION × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ZXE Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (OC) Deposited 2022-05-20 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 × 8 PDB declaration: decameric
Chain M 1–316（316 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8BVW RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) Deposited 2022-12-20 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 × 40 PDB declaration: 42-meric
Chain M 1–316（316 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8BYQ RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W) Deposited 2022-12-14 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 × 38 PDB declaration: 40-meric
Chain M 1–316（316 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8BZ1 RNA polymerase II core pre-initiation complex with the proximal +1 nucleosome (cPIC-Nuc10W) Deposited 2022-12-14 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 × 26 PDB declaration: 28-meric
Chain M 1–316（316 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8GXQ PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state Deposited 2022-09-21 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 × 83 PDB declaration: 87-meric
Chain BA 1–316（316 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 mutation/modification 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 BA 1–316（316 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
8S51 RNA polymerase II core initially transcribing complex with an ordered RNA of 8 nt Deposited 2024-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain M 1–316（316 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8S52 RNA polymerase II core initially transcribing complex with an ordered RNA of 10 nt Deposited 2024-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain M 1–316（316 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8S5N RNA polymerase II core initially transcribing complex with an ordered RNA of 12 nt Deposited 2024-02-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain M 1–316（316 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 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 mutation/modification 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 R 1–316（316 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 mutation/modification 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 R 1–316（316 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 mutation/modification 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 R 1–316（316 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 mutation/modification 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 R 1–316（316 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 mutation/modification 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 R 1–316（316 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 mutation/modification 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 R 1–316（316 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 mutation/modification 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 R 1–316（316 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 mutation/modification 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 R 1–316（316 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

54 other PDB entries and 61 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TF2B_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–206； UniProt 112–316

Alpha trans-inducing protein

Herpes simplex virus (type 1 / strain 17)

UniProt P06492

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 465–490 Fragment：part of activation domain Transcription initiation factor IIB × 1 （Q00403） SOLUTION NMR NMR measurement conditions：pH 5.6；298 K；Ionic strength (raw mmCIF value) 100 mM；Pressure 1 NMR sample composition：0.2 mM VP16ad U-15N, 0-0.2 mM TFIIBc, 50 mM KCl, 50 mM phosphate buffer pH 5.6, 95% H2O, 5% D2O | 95% H2O/5% D2O Resolution not provided

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 2PHG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
16VP CONSERVED CORE OF THE HERPES SIMPLEX VIRUS TRANSCRIPTIONAL REGULATORY PROTEIN VP16 Deposited 1999-02-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 47–412（366 aa） Fragment：CONSERVED CORE
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4；pH 4.0
Resolution 2.10 Å R-free 0.260
2PHE Model for VP16 binding to PC4 Deposited 2007-04-11 Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 465–490（26 aa） Fragment：part of activation domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.6；298 K；Ionic strength (raw mmCIF value) 100-450 mM；Pressure 1
NMR measurement conditions pH 5.6；305 K；Ionic strength (raw mmCIF value) 100-450 mM；Pressure 1
NMR sample composition 0.2 mM VP16ad U-15N or U15N,13C, 0-0.5 mM PC4 or PC4ctd, 50 or 400 mM KCl, 50 mM phosphate buffer pH 5.6, 2 M D6-Glycine, H2O | H2O
NMR sample composition 0.2 mM PC4 or PC4ctd U-15N, 0-0.5 mM VP16ad, 50 or 400 mM KCl, 50 mM phosphate buffer pH 5.6, 2 M D6-Glycine, H2O | H2O
Resolution not provided

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ATIN_HHV11
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–26； UniProt 465–490

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

SAXS profile for 2phg

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2phg
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id2phg
Deposition date deposition_date2007-04-11
Structure title titleModel for VP16 binding to TFIIB
Keywords keywordsTF2B, VP16, transcription, activator; TRANSCRIPTION
Experimental Method methodSOLUTION NMR
▼

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

Radius of gyration Rg (Guinier) rg_guinier18.04 Å
Radius of gyration Rg (electron density) rg_electron17.72 Å
Forward intensity I(0) i0931820000.00
Molecular weight molecular_weight258730.0 kDa
Excluded volume excluded_volume324670 ų
Envelope volume envelope_volume58386 ų
Hydration-shell volume shell_volume23940 ų
Envelope diameter envelope_diameter67.0 Å
Shell Rg shell_rg27.23 Å
Envelope Rg envelope_rg19.99 Å
Shape Rg shape_rg17.68 Å
Total Rg total_rg18.08 Å
Total atoms total_atoms18110
Residues n_residues2320
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

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

Maximum dimension Dmax dmax59.8 Å
Rg (real space) rg_real17.95 Å
Rg uncertainty (real space) rg_real_error0.40 Å
I(0) (real space) i0_real9.3180e+08
I(0) uncertainty (real space) i0_real_error1.1150e+07
Rg (reciprocal space) rg_reciprocal17.96 Å
I(0) (reciprocal space) i0_reciprocal931800000.0000
Solution quality estimate total_estimate0.7910
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary23.4 Å
Skewness Skewness skewness0.244
Kurtosis Kurtosis kurtosis-0.297
Angular range angular_range— – 0.4400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2983000.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.769; Stabil: 0.991; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd2phga1
Class classa — All alpha proteins
Fold Fold folda.74 — Cyclin-like
Superfamily Superfamily superfamilya.74.1 — Cyclin-like
Family Family familya.74.1.2 — Transcription factor IIB (TFIIB), core domain
Domain ID domain_idd2phga2
Class classa — All alpha proteins
Fold Fold folda.74 — Cyclin-like
Superfamily Superfamily superfamilya.74.1 — Cyclin-like
Family Family familya.74.1.2 — Transcription factor IIB (TFIIB), core domain
Domain ID domain_idd2phga3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id2phgA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily10 — Cyclin-like
Domain ID domain_id2phgA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily10 — Cyclin-like
▶

8. Citations (1)

▶

9. Files and Curves (10)