› 8wb0

Electron Microscopy
2.94Å resolution

De novo transcribing complex 17 (TC17), the early elongation complex with Pol II positioned 17nt downstream of TSS

Released:
DOI: 10.2210/pdb8wb0/pdb
PDB entry 8wb0 coloured by chain, front view.
PDB entry 8wb0 coloured by chain, side view.
PDB entry 8wb0 coloured by chain, top view.
Source organisms:
Primary publication:
Structural visualization of transcription initiation in action.
Chen X, Liu W, Wang Q, Wang X, Ren Y, Qu X, Li W, Xu Y
Science 382 eadi5120 (2023)
PMID: 38127763
Related structures: EMD-37411

Function and Biology Details

Reactions catalysed: 
ATP + H(2)O = ADP + phosphate
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero octadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-283571 (preferred)
Entry contents:
15 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (18 distinct):
Alpha-amanitin Chain: N
Molecule details ›
Chain: N
Length: 8 amino acids
Theoretical weight: 939 Da
Source organism: Amanita phalloides
UniProt:
  • Canonical: P85421 (Residues: 1-8; Coverage: 35%)
General transcription factor IIF subunit 1 Chain: S
Molecule details ›
Chain: S
Length: 517 amino acids
Theoretical weight: 58.34 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
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: T
Molecule details ›
Chain: T
Length: 249 amino acids
Theoretical weight: 28.43 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P13984 (Residues: 1-249; Coverage: 100%)
Gene names: GTF2F2, RAP30
Sequence domains:
DNA-directed RNA polymerase subunit Chain: o
Molecule details ›
Chain: o
Length: 1970 amino acids
Theoretical weight: 217.45 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D1DPV6 (Residues: 1-1970; Coverage: 100%)
Gene name: POLR2A
Sequence domains:
DNA-directed RNA polymerase subunit beta Chain: p
Molecule details ›
Chain: p
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: q
Molecule details ›
Chain: q
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: r
Molecule details ›
Chain: r
Length: 142 amino acids
Theoretical weight: 16.33 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VM56 (Residues: 1-142; Coverage: 100%)
Gene name: POLR2D
Sequence domains: RNA polymerase Rpb4
DNA-directed RNA polymerase II subunit E Chain: s
Molecule details ›
Chain: s
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: t
Molecule details ›
Chain: t
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 subunit Chain: u
Molecule details ›
Chain: u
Length: 172 amino acids
Theoretical weight: 19.31 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VKG7 (Residues: 1-172; Coverage: 100%)
Gene name: POLR2G
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC3 Chain: v
Molecule details ›
Chain: v
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: w
Molecule details ›
Chain: w
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: x
Molecule details ›
Chain: x
Length: 67 amino acids
Theoretical weight: 7.66 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8W4F9W9 (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: y
Molecule details ›
Chain: y
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: RNA polymerase Rpb3/Rpb11 dimerisation domain
DNA-directed RNA polymerases I, II, and III subunit RPABC4 Chain: z
Molecule details ›
Chain: z
Length: 58 amino acids
Theoretical weight: 7.02 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D0JYF1 (Residues: 1-58; Coverage: 100%)
Gene name: POLR2K
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit
non-template DNA Chain: X
Molecule details ›
Chain: X
Length: 99 nucleotides
Theoretical weight: 30.63 KDa
template DNA Chain: Y
Molecule details ›
Chain: Y
Length: 99 nucleotides
Theoretical weight: 30.46 KDa
RNA Chain: Z
Molecule details ›
Chain: Z
Length: 13 nucleotides
Theoretical weight: 4.1 KDa

Ligands and Environments

3 bound ligands:
Ligand ZN 8 x ZN
Ligand MG 1 x MG
Ligand W0F 1 x W0F
5 modified residues:
Ligand ILX 1 x ILX
Ligand TRX 1 x TRX
Ligand CSX 1 x CSX
Ligand HYP 1 x HYP
Ligand G2L 1 x G2L

Experiments and Validation Details

Entry percentile scores
Resolution: 2.94Å
Relevant EMDB volumes: EMD-37411
Expression system: Homo sapiens

Quick links