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1d8j

SOLUTION STRUCTURE OF THE CENTRAL CORE DOMAIN OF TFIIE BETA

Method: SOLUTION NMR Dmax: 33.3 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

GENERAL TRANSCRIPTION FACTOR TFIIE-BETA

Homo sapiens

UniProt P29084

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 66–146 Fragment：CENTRAL CORE DOMAIN No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6；300 K；Ionic strength (raw mmCIF value) 500mM NACL；Pressure AMBIENT NMR sample composition：1-2MM PROTEIN U-15N,13C; 20MM PHOSPHATE BUFFER, 500MM NACL NMR sample composition：1-2MM PROTEIN ; 20MM PHOSPHATE BUFFER, 500MM NACL 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 1D8J Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1D8K SOLUTION STRUCTURE OF THE CENTRAL CORE DOMAIN OF TFIIE BETA Deposited 1999-10-25 Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 66–146（81 aa） Fragment：CENTRAL CORE DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；300 K；Ionic strength (raw mmCIF value) 500mM NACL；Pressure AMBIENT
NMR sample composition 1-2MM PROTEIN U-15N,13C; 20MM PHOSPHATE BUFFER, 500MM NACL
NMR sample composition 1-2MM PROTEIN U-15N; 20MM PHOSPHATE BUFFER, 500MM NACL
NMR sample composition 1-2MM PROTEIN ; 20MM PHOSPHATE BUFFER, 500MM NACL
Resolution not provided
5GPY Crystal structure of the human TFIIE 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 heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 141–244（104 aa） Fragment：UNP residues 141-244
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.9；293 K；12% PEG3350
Resolution 2.10 Å R-free 0.237
5IY6 Human holo-PIC in the closed state Deposited 2016-03-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain R 1–291（291 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 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 R 1–291（291 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 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 R 1–291（291 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 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 R 1–291（291 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 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 R 1–291（291 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 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 R 1–291（291 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 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 R 1–291（291 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 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 R 1–291（291 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
6O9L Human holo-PIC in the closed state Deposited 2019-03-14 Different construct 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 R 1–291（291 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
7EG9 TFIID-based intermediate PIC on SCP promoter Deposited 2021-03-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 39 PDB declaration: 41-meric
Chain V 1–291（291 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7EGA TFIID-based intermediate PIC on PUMA promoter Deposited 2021-03-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 39 PDB declaration: 41-meric
Chain V 1–291（291 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7EGB TFIID-based holo PIC on SCP promoter Deposited 2021-03-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain V 1–291（291 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7EGC p53-bound TFIID-based holo PIC on HDM2 promoter Deposited 2021-03-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain V 1–291（291 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 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 EB 1–291（291 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.07 Å
7ENC TFIID-based PIC-Mediator holo-complex in fully-assembled state (hPIC-MED) Deposited 2021-04-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 74 PDB declaration: 76-meric
Chain EB 1–291（291 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 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 R 1–291（291 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 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 X 1–291（291 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 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 X 1–291（291 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 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 X 1–291（291 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 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 X 1–291（291 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 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 X 1–291（291 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 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 X 1–291（291 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 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 X 1–291（291 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
8BVW RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) Deposited 2022-12-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain X 1–291（291 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 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 X 1–291（291 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
8GXQ PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state Deposited 2022-09-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric
Chain EB 1–291（291 aa）
Not recorded ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.04 Å
8GXS PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state Deposited 2022-09-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric
Chain EB 1–291（291 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 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 X 1–291（291 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 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 X 1–291（291 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
8S55 RNA polymerase II early elongation complex bound to TFIIE and TFIIF - state a (composite structure) Deposited 2024-02-22 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: 19-meric
Chain X 1–291（291 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 3.40 Å
8S5N RNA polymerase II core initially transcribing complex with an ordered RNA of 12 nt Deposited 2024-02-24 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 X 1–291（291 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 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 V 1–291（291 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.47 Å
8WAL Structure of transcribing complex 3 (TC3), the initially transcribing complex with Pol II positioned 3nt downstream of TSS. Deposited 2023-09-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain V 1–291（291 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.52 Å
8WAN Structure of transcribing complex 4 (TC4), the initially transcribing complex with Pol II positioned 4nt downstream of TSS. Deposited 2023-09-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain V 1–291（291 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.07 Å
8WAO Structure of transcribing complex 5 (TC5), the initially transcribing complex with Pol II positioned 5nt downstream of TSS. Deposited 2023-09-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain V 1–291（291 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
8WAP Structure of transcribing complex 6 (TC6), the initially transcribing complex with Pol II positioned 6nt downstream of TSS. Deposited 2023-09-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain V 1–291（291 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.85 Å
8WAQ Structure of transcribing complex 7 (TC7), the initially transcribing complex with Pol II positioned 7nt downstream of TSS. Deposited 2023-09-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain V 1–291（291 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.29 Å
8WAR Structure of transcribing complex 8 (TC8), the initially transcribing complex with Pol II positioned 8nt downstream of TSS. Deposited 2023-09-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain V 1–291（291 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
8WAS Structure of transcribing complex 9 (TC9), the initially transcribing complex with Pol II positioned 9nt downstream of TSS. Deposited 2023-09-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain V 1–291（291 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

41 other PDB entries and 41 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name T2EB_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–81； UniProt 66–146

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 1d8j

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1d8j
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1d8j
Deposition date deposition_date1999-10-25
Structure title titleSOLUTION STRUCTURE OF THE CENTRAL CORE DOMAIN OF TFIIE BETA
Keywords keywordsWINGED HELIX-TURN-HELIX, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, GENE REGULATION; GENE REGULATION
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier13.03 Å
Radius of gyration Rg (electron density) rg_electron12.81 Å
Forward intensity I(0) i0453739000.00
Molecular weight molecular_weight185510.0 kDa
Excluded volume excluded_volume234850 ų
Envelope volume envelope_volume31179 ų
Hydration-shell volume shell_volume15441 ų
Envelope diameter envelope_diameter62.2 Å
Shell Rg shell_rg23.11 Å
Envelope Rg envelope_rg18.06 Å
Shape Rg shape_rg12.78 Å
Total Rg total_rg13.19 Å
Total atoms total_atoms26460
Residues n_residues1620
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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax33.3 Å
Rg (real space) rg_real12.39 Å
Rg uncertainty (real space) rg_real_error0.04 Å
I(0) (real space) i0_real4.3410e+08
I(0) uncertainty (real space) i0_real_error3.1630e+06
Rg (reciprocal space) rg_reciprocal13.04 Å
I(0) (reciprocal space) i0_reciprocal453700000.0000
Solution quality estimate total_estimate0.6824
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary15.6 Å
Skewness Skewness skewness0.132
Kurtosis Kurtosis kurtosis-0.354
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha3.3570
Highest regularization parameter α highest_alpha129800.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.001; Oscil: 0.975; Stabil: 0.984; Sysdev: 0.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1d8ja_
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.5 — 'Winged helix' DNA-binding domain
Family Family familya.4.5.18 — The central core domain of TFIIE beta

CATH v4.4 (1 domains)

Domain ID domain_id1d8jA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
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8. Citations (1)

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9. Files and Curves (10)