› 8bz1

Electron Microscopy
3.8Å resolution

RNA polymerase II core pre-initiation complex with the proximal +1 nucleosome (cPIC-Nuc10W)

Released:
DOI: 10.2210/pdb8bz1/pdb
PDB entry 8bz1 coloured by chain, front view.
PDB entry 8bz1 coloured by chain, side view.
PDB entry 8bz1 coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of transcription reduction by a promoter-proximal +1 nucleosome.
Abril-Garrido J, Dienemann C, Grabbe F, Velychko T, Lidschreiber M, Wang H, Cramer P
OpenAccess logo Mol Cell (2023)
PMID: 37148879
Related structures: EMD-16335

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 28-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-496482 (preferred)
Entry contents:
22 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (24 distinct):
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: A0A8D1DPV6 (Residues: 1-1970; Coverage: 100%)
Gene name: POLR2A
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: RNA polymerase Rpb3/Rpb11 dimerisation domain
RNA polymerase II, I and III subunit K 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:
Histone H3.2 Chains: a, e
Molecule details ›
Chains: a, e
Length: 136 amino acids
Theoretical weight: 15.44 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 1-136; Coverage: 100%)
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: b, f
Molecule details ›
Chains: b, f
Length: 103 amino acids
Theoretical weight: 11.39 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 1-103; Coverage: 100%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A type 1 Chains: c, g
Molecule details ›
Chains: c, g
Length: 130 amino acids
Theoretical weight: 14.09 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 1-130; Coverage: 100%)
Sequence domains:
Histone H2B 1.1 Chains: d, h
Molecule details ›
Chains: d, h
Length: 126 amino acids
Theoretical weight: 13.97 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 1-126; Coverage: 100%)
Sequence domains: Core histone H2A/H2B/H3/H4
Non-template DNA Chain: N
Molecule details ›
Chain: N
Length: 210 nucleotides
Theoretical weight: 64.78 KDa
Template DNA Chain: T
Molecule details ›
Chain: T
Length: 210 nucleotides
Theoretical weight: 64.91 KDa

Ligands and Environments

2 bound ligands:
Ligand ZN 9 x ZN
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.8Å
Relevant EMDB volumes: EMD-16335
Expression systems:
  • Escherichia coli
  • Trichoplusia ni

Quick links

Citations

2 review citations

Transcription factor IID parks and drives preinitiation complexes at sharp or broad promoters.
Bernardini et al. (2023)
1 more

1 mention without citation

Structural basis of transcription reduction by a promoter-proximal +1 nucleosome.
Abril-Garrido et al. (2023)