› 7wbv

Electron Microscopy
4.1Å resolution

RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome

Released:
DOI: 10.2210/pdb7wbv/pdb
PDB entry 7wbv coloured by chain, front view.
PDB entry 7wbv coloured by chain, side view.
PDB entry 7wbv coloured by chain, top view.
Source organisms:
Primary publication:
Structural Basis of Damaged Nucleotide Recognition by Transcribing RNA Polymerase II in the Nucleosome.
Osumi K, Kujirai T, Ehara H, Ogasawara M, Kinoshita C, Saotome M, Kagawa W, Sekine SI, Takizawa Y, Kurumizaka H
J Mol Biol 435 168130 (2023)
PMID: 37120012
Related structures: EMD-32407

Function and Biology Details

Reaction catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero 26-mer (preferred)
PDBe Complex ID:
PDB-CPX-235613 (preferred)
Entry contents:
19 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (22 distinct):
DNA-directed RNA polymerase subunit Chain: A
Molecule details ›
Chain: A
Length: 1743 amino acids
Theoretical weight: 194.11 KDa
Source organism: Komagataella phaffii
UniProt:
  • Canonical: C4R4Y0 (Residues: 1-1743; Coverage: 100%)
Gene name: PAS_chr3_0568
Sequence domains:
DNA-directed RNA polymerase subunit beta Chain: B
Molecule details ›
Chain: B
Length: 1227 amino acids
Theoretical weight: 139.75 KDa
Source organism: Komagataella phaffii
Expression system: Komagataella pastoris
UniProt:
  • Canonical: C4QZQ7 (Residues: 1-1227; Coverage: 100%)
Gene name: PAS_chr2-1_0125
Sequence domains:
DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein Chain: C
Molecule details ›
Chain: C
Length: 304 amino acids
Theoretical weight: 34.22 KDa
Source organism: Komagataella phaffii
Expression system: Komagataella pastoris
UniProt:
  • Canonical: C4R7L2 (Residues: 1-304; Coverage: 100%)
Gene name: PAS_chr4_0344
Sequence domains:
RNA polymerase Rpb4/RPC9 core domain-containing protein Chain: D
Molecule details ›
Chain: D
Length: 186 amino acids
Theoretical weight: 20.62 KDa
Source organism: Komagataella phaffii
UniProt:
  • Canonical: C4R2U9 (Residues: 1-186; Coverage: 100%)
Gene name: PAS_chr2-2_0104
Sequence domains: RNA polymerase Rpb4
DNA-directed RNA polymerases I, II, and III subunit RPABC1 Chain: E
Molecule details ›
Chain: E
Length: 214 amino acids
Theoretical weight: 24.96 KDa
Source organism: Komagataella phaffii
UniProt:
  • Canonical: C4R3P8 (Residues: 1-214; Coverage: 100%)
Gene name: PAS_chr3_0157
Sequence domains:
RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III Chain: F
Molecule details ›
Chain: F
Length: 155 amino acids
Theoretical weight: 17.8 KDa
Source organism: Komagataella phaffii
UniProt:
  • Canonical: C4R1V1 (Residues: 1-155; Coverage: 100%)
Gene name: PAS_chr2-2_0434
Sequence domains: RNA polymerase Rpb6
DNA-directed RNA polymerase subunit Chain: G
Molecule details ›
Chain: G
Length: 171 amino acids
Theoretical weight: 18.8 KDa
Source organism: Komagataella phaffii
UniProt:
  • Canonical: C4R9A1 (Residues: 1-171; Coverage: 100%)
Gene name: PAS_chr4_0906
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC3 Chain: H
Molecule details ›
Chain: H
Length: 145 amino acids
Theoretical weight: 16.25 KDa
Source organism: Komagataella phaffii
UniProt:
  • Canonical: C4R273 (Residues: 1-145; Coverage: 100%)
Gene name: PAS_chr2-2_0309
Sequence domains: RNA polymerase Rpb8
DNA-directed RNA polymerase subunit Chain: I
Molecule details ›
Chain: I
Length: 115 amino acids
Theoretical weight: 13.61 KDa
Source organism: Komagataella phaffii
UniProt:
  • Canonical: F2QPE6 (Residues: 1-115; Coverage: 100%)
Gene names: PP7435_Chr1-1144, RPB9
Sequence domains:
RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III Chain: J
Molecule details ›
Chain: J
Length: 72 amino acids
Theoretical weight: 8.55 KDa
Source organism: Komagataella phaffii
UniProt:
  • Canonical: C4R009 (Residues: 1-72; Coverage: 100%)
Gene name: PAS_chr2-1_0223
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: 118 amino acids
Theoretical weight: 13.83 KDa
Source organism: Komagataella phaffii
UniProt:
  • Canonical: C4R3Z5 (Residues: 1-118; Coverage: 100%)
Gene name: PAS_chr3_0244
Sequence domains: RNA polymerase Rpb3/Rpb11 dimerisation domain
RNA polymerase subunit ABC10-alpha Chain: L
Molecule details ›
Chain: L
Length: 72 amino acids
Theoretical weight: 7.86 KDa
Source organism: Komagataella phaffii
UniProt:
  • Canonical: F2QMI1 (Residues: 1-72; Coverage: 100%)
Gene names: PP7435_Chr1-0476, RPC10
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit
Transcription elongation factor 1 homolog Chain: M
Molecule details ›
Chain: M
Length: 113 amino acids
Theoretical weight: 12.61 KDa
Source organism: Komagataella phaffii
Expression system: Escherichia coli
UniProt:
  • Canonical: C4QZ45 (Residues: 1-110; Coverage: 100%)
Gene name: PAS_c121_0006
Sequence domains: Transcription elongation factor Elf1 like
Transcription elongation factor SPT4 Chain: V
Molecule details ›
Chain: V
Length: 108 amino acids
Theoretical weight: 12.04 KDa
Source organism: Komagataella phaffii
Expression system: Escherichia coli
UniProt:
  • Canonical: C4R0E6 (Residues: 7-114; Coverage: 95%)
Gene name: PAS_chr2-1_0350
Sequence domains: Spt4/RpoE2 zinc finger
Transcription elongation factor SPT5 Chain: W
Molecule details ›
Chain: W
Length: 812 amino acids
Theoretical weight: 91.35 KDa
Source organism: Komagataella phaffii
Expression system: Escherichia coli
UniProt:
  • Canonical: C4R370 (Residues: 1-809; Coverage: 89%)
Gene name: PAS_chr3_1136
Sequence domains:
Histone H3.3 Chains: a, e
Molecule details ›
Chains: a, e
Length: 139 amino acids
Theoretical weight: 15.64 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P84243 (Residues: 1-136; Coverage: 100%)
Gene names: H3-3A, H3-3B, H3.3A, H3.3B, H3F3, H3F3A, H3F3B, PP781
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: b, f
Molecule details ›
Chains: b, f
Length: 106 amino acids
Theoretical weight: 11.68 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62805 (Residues: 2-103; Coverage: 99%)
Gene names: H4-16, H4/A, H4/B, H4/C, H4/D, H4/E, H4/G, H4/H, H4/I, H4/J, H4/K, H4/M, H4/N, H4/O, H4C1, H4C11, H4C12, H4C13, H4C14, H4C15, H4C16, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4F2, H4FA, H4FB, H4FC, H4FD, H4FE, H4FG, H4FH, H4FI, H4FJ, H4FK, H4FM, H4FN, H4FO, HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4, HIST2H4A, HIST2H4B, HIST4H4
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A type 1-B/E Chains: c, g
Molecule details ›
Chains: c, g
Length: 133 amino acids
Theoretical weight: 14.45 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P04908 (Residues: 2-130; Coverage: 99%)
Gene names: H2AC4, H2AC8, H2AFA, H2AFM, HIST1H2AB, HIST1H2AE
Sequence domains:
Histone H2B type 1-J Chains: d, h
Molecule details ›
Chains: d, h
Length: 129 amino acids
Theoretical weight: 14.22 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P06899 (Residues: 2-126; Coverage: 99%)
Gene names: H2BC11, H2BFR, HIST1H2BJ
Sequence domains: Core histone H2A/H2B/H3/H4
DNA (198-MER) Chain: N
Molecule details ›
Chain: N
Length: 198 nucleotides
Theoretical weight: 61.38 KDa
DNA (159-MER) Chain: T
Molecule details ›
Chain: T
Length: 198 nucleotides
Theoretical weight: 60.85 KDa
RNA (5'-R(P*UP*GP*GP*CP*CP*GP*UP*UP*UP*UP*CP*GP*UP*UP*GP*U)-3') Chain: P
Molecule details ›
Chain: P
Length: 16 nucleotides
Theoretical weight: 5.05 KDa

Ligands and Environments

2 bound ligands:
Ligand ZN 10 x ZN
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.1Å
Relevant EMDB volumes: EMD-32407
Expression systems:
  • Komagataella pastoris
  • Escherichia coli

Quick links

Citations

1 citations in other articles

Elf1 promotes Rad26's interaction with lesion-arrested Pol II for transcription-coupled repair.
Sarsam et al. (2024)