› 7nw0

Electron Microscopy
6.6Å resolution

RNA polymerase II pre-initiation complex with open promoter DNA

Released:
DOI: 10.2210/pdb7nw0/pdb
PDB entry 7nw0 coloured by chain, front view.
PDB entry 7nw0 coloured by chain, side view.
PDB entry 7nw0 coloured by chain, top view.
Source organisms:
Primary publication:
Structures of mammalian RNA polymerase II pre-initiation complexes.
Aibara S, Schilbach S, Cramer P
Nature 594 124-128 (2021)
PMID: 33902107
Related structures: EMD-12619

Function and Biology Details

Reactions catalysed: 
ATP + H(2)O = ADP + phosphate
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Acetyl-CoA + [protein]-L-lysine = CoA + [protein]-N(6)-acetyl-L-lysine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 32-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-236749 (preferred)
Entry contents:
30 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (32 distinct):
General transcription and DNA repair factor IIH helicase subunit XPD Chain: 0
Molecule details ›
Chain: 0
Length: 760 amino acids
Theoretical weight: 87.02 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P18074 (Residues: 1-760; Coverage: 100%)
Gene names: ERCC2, XPD, XPDC
Sequence domains:
General transcription factor IIH subunit 1 Chain: 1
Molecule details ›
Chain: 1
Length: 548 amino acids
Theoretical weight: 62.12 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P32780 (Residues: 1-548; Coverage: 100%)
Gene names: BTF2, GTF2H1
Sequence domains:
General transcription factor IIH subunit 4 Chain: 2
Molecule details ›
Chain: 2
Length: 462 amino acids
Theoretical weight: 52.25 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q92759 (Residues: 1-462; Coverage: 100%)
Gene name: GTF2H4
Sequence domains:
CDK-activating kinase assembly factor MAT1 Chain: 3
Molecule details ›
Chain: 3
Length: 309 amino acids
Theoretical weight: 35.87 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P51948 (Residues: 1-309; Coverage: 100%)
Gene names: CAP35, MAT1, MNAT1, RNF66
Sequence domains:
General transcription factor IIH subunit 3 Chain: 4
Molecule details ›
Chain: 4
Length: 308 amino acids
Theoretical weight: 34.42 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q13889 (Residues: 1-308; Coverage: 100%)
Gene name: GTF2H3
Sequence domains: Transcription factor Tfb4
General transcription factor IIH subunit 5 Chain: 5
Molecule details ›
Chain: 5
Length: 71 amino acids
Theoretical weight: 8.06 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q6ZYL4 (Residues: 1-71; Coverage: 100%)
Gene names: C6orf175, GTF2H5, TTDA
Sequence domains: Transcription factor TFIIH complex subunit Tfb5
General transcription factor IIH subunit 2 Chain: 6
Molecule details ›
Chain: 6
Length: 395 amino acids
Theoretical weight: 44.48 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q13888 (Residues: 1-395; Coverage: 100%)
Gene names: BTF2P44, GTF2H2
Sequence domains:
General transcription and DNA repair factor IIH helicase/translocase subunit XPB Chain: 7
Molecule details ›
Chain: 7
Length: 782 amino acids
Theoretical weight: 89.4 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P19447 (Residues: 1-782; Coverage: 100%)
Gene names: ERCC3, XPB, XPBC
Sequence domains:
DNA-directed RNA polymerase subunit Chain: A
Molecule details ›
Chain: A
Length: 1970 amino acids
Theoretical weight: 217.45 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A7M4DUC2 (Residues: 1-1984; Coverage: 99%)
Sequence domains:
DNA-directed RNA polymerase subunit beta Chain: B
Molecule details ›
Chain: B
Length: 1174 amino acids
Theoretical weight: 134.04 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LGP4 (Residues: 127-1300; Coverage: 90%)
Gene name: POLR2B
Sequence domains:
DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein Chain: C
Molecule details ›
Chain: C
Length: 275 amino acids
Theoretical weight: 31.44 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LCH3 (Residues: 1-275; Coverage: 100%)
Gene name: POLR2C
Sequence domains:
RNA polymerase Rpb4/RPC9 core domain-containing protein Chain: D
Molecule details ›
Chain: D
Length: 142 amino acids
Theoretical weight: 16.33 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287ADR4 (Residues: 43-184; Coverage: 77%)
Gene name: POLR2D
Sequence domains: RNA polymerase Rpb4
DNA-directed RNA polymerase II subunit E Chain: E
Molecule details ›
Chain: E
Length: 210 amino acids
Theoretical weight: 24.64 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LSI7 (Residues: 1-210; Coverage: 100%)
Gene name: POLR2E
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC2 Chain: F
Molecule details ›
Chain: F
Length: 127 amino acids
Theoretical weight: 14.48 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VEK9 (Residues: 1-127; Coverage: 100%)
Gene name: POLR2F
Sequence domains: RNA polymerase Rpb6
DNA-directed RNA polymerase II subunit RPB7 Chain: G
Molecule details ›
Chain: G
Length: 172 amino acids
Theoretical weight: 19.31 KDa
Source organism: Sus scrofa
DNA-directed RNA polymerases I, II, and III subunit RPABC3 Chain: H
Molecule details ›
Chain: H
Length: 150 amino acids
Theoretical weight: 17.16 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LCB2 (Residues: 1-150; Coverage: 100%)
Gene name: POLR2H
Sequence domains: RNA polymerase Rpb8
DNA-directed RNA polymerase II subunit RPB9 Chain: I
Molecule details ›
Chain: I
Length: 125 amino acids
Theoretical weight: 14.54 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: P60899 (Residues: 1-125; Coverage: 100%)
Gene name: POLR2I
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC5 Chain: J
Molecule details ›
Chain: J
Length: 67 amino acids
Theoretical weight: 7.66 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VYD0 (Residues: 1-67; Coverage: 100%)
Gene name: POLR2L
Sequence domains: RNA polymerases N / 8 kDa subunit
DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein Chain: K
Molecule details ›
Chain: K
Length: 117 amino acids
Theoretical weight: 13.31 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RKE4 (Residues: 1-117; Coverage: 100%)
Gene name: POLR2J
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC4 Chain: L
Molecule details ›
Chain: L
Length: 58 amino acids
Theoretical weight: 7.02 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1TRS6 (Residues: 1-58; Coverage: 100%)
Gene name: POLR2K
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit
Transcription initiation factor IIB Chain: M
Molecule details ›
Chain: M
Length: 316 amino acids
Theoretical weight: 34.88 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q00403 (Residues: 1-316; Coverage: 100%)
Gene names: GTF2B, TF2B, TFIIB
Sequence domains:
TATA-box-binding protein Chain: O
Molecule details ›
Chain: O
Length: 339 amino acids
Theoretical weight: 37.73 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P20226 (Residues: 1-339; Coverage: 100%)
Gene names: GTF2D1, TBP, TF2D, TFIID
Sequence domains: Transcription factor TFIID (or TATA-binding protein, TBP)
General transcription factor IIF subunit 1 Chain: Q
Molecule details ›
Chain: Q
Length: 517 amino acids
Theoretical weight: 58.34 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P35269 (Residues: 1-517; Coverage: 100%)
Gene names: GTF2F1, RAP74
Sequence domains: Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)
General transcription factor IIF subunit 2 Chain: R
Molecule details ›
Chain: R
Length: 249 amino acids
Theoretical weight: 28.43 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P13984 (Residues: 1-249; Coverage: 100%)
Gene names: GTF2F2, RAP30
Sequence domains:
Transcription initiation factor IIA subunit 1 Chain: U
Molecule details ›
Chain: U
Length: 376 amino acids
Theoretical weight: 41.54 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P52655 (Residues: 1-376; Coverage: 100%)
Gene names: GTF2A1, TF2A1
Sequence domains: Transcription factor IIA, alpha/beta subunit
Transcription initiation factor IIA subunit 2 Chain: V
Molecule details ›
Chain: V
Length: 109 amino acids
Theoretical weight: 12.47 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P52657 (Residues: 1-109; Coverage: 100%)
Gene names: GTF2A2, TF2A2
Sequence domains:
General transcription factor IIE subunit 1 Chain: W
Molecule details ›
Chain: W
Length: 439 amino acids
Theoretical weight: 49.52 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P29083 (Residues: 1-439; Coverage: 100%)
Gene names: GTF2E1, TF2E1
Sequence domains:
Transcription initiation factor IIE subunit beta Chain: X
Molecule details ›
Chain: X
Length: 291 amino acids
Theoretical weight: 33.11 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P29084 (Residues: 1-291; Coverage: 100%)
Gene names: GTF2E2, TF2E2
Sequence domains:
Unassigned peptide, likely TFIIE-Beta Chain: Y
Molecule details ›
Chain: Y
Length: 16 amino acids
Theoretical weight: 1.38 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Unassigned peptide, likely XPB Chain: Z
Molecule details ›
Chain: Z
Length: 8 amino acids
Theoretical weight: 699 Da
Source organism: Homo sapiens
Expression system: Trichoplusia ni
Non-template DNA Chain: N
Molecule details ›
Chain: N
Length: 106 nucleotides
Theoretical weight: 32.91 KDa
Template DNA Chain: T
Molecule details ›
Chain: T
Length: 106 nucleotides
Theoretical weight: 32.51 KDa

Ligands and Environments

5 bound ligands:
Ligand SF4 1 x SF4
Ligand ZN 15 x ZN
Ligand ADP 1 x ADP
Ligand MG 2 x MG
Ligand BEF 1 x BEF
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 6.6Å
Relevant EMDB volumes: EMD-12619
Expression systems:
  • Trichoplusia ni
  • Escherichia coli

Quick links

Citations

8 review citations

The Mediator complex as a master regulator of transcription by RNA polymerase II.
Richter et al. (2022)
7 more

1 mention without citation

Lesion recognition by XPC, TFIIH and XPA in DNA excision repair.
Kim et al. (2023)