› 8jh2

Electron Microscopy
5.7Å resolution

RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome

Released:
DOI: 10.2210/pdb8jh2/pdb
PDB entry 8jh2 coloured by chain, front view.
PDB entry 8jh2 coloured by chain, side view.
PDB entry 8jh2 coloured by chain, top view.
Source organisms:
Primary publication:
Cryo-EM structures of RNA polymerase II-nucleosome complexes rewrapping transcribed DNA.
Akatsu M, Ehara H, Kujirai T, Fujita R, Ito T, Osumi K, Ogasawara M, Takizawa Y, Sekine SI, Kurumizaka H
OpenAccess logo J Biol Chem 105477 (2023)
PMID: 37981206
Related structures: EMD-36251

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 28-mer (preferred)
PDBe Complex ID:
PDB-CPX-270089 (preferred)
Entry contents:
19 distinct polypeptide molecules
4 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (24 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
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
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:
DNA-directed RNA polymerases I, II, and III subunit RPABC5 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: 110 amino acids
Theoretical weight: 12.4 KDa
Source organism: Komagataella phaffii
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: 114 amino acids
Theoretical weight: 12.63 KDa
Source organism: Komagataella phaffii
Expression system: Escherichia coli
UniProt:
  • Canonical: C4R0E6 (Residues: 1-114; Coverage: 100%)
Gene name: PAS_chr2-1_0350
Sequence domains: Spt4/RpoE2 zinc finger
Transcription elongation factor SPT5 Chain: W
Molecule details ›
Chain: W
Length: 908 amino acids
Theoretical weight: 101.25 KDa
Source organism: Komagataella phaffii
Expression system: Escherichia coli
UniProt:
  • Canonical: C4R370 (Residues: 1-908; Coverage: 100%)
Gene name: PAS_chr3_1136
Sequence domains:
Histone H3.3 Chains: a, e
Molecule details ›
Chains: a, e
Length: 136 amino acids
Theoretical weight: 15.36 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: 103 amino acids
Theoretical weight: 11.39 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62805 (Residues: 1-103; Coverage: 100%)
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: 130 amino acids
Theoretical weight: 14.17 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P04908 (Residues: 1-130; Coverage: 100%)
Gene names: H2AC4, H2AC8, H2AFA, H2AFM, HIST1H2AB, HIST1H2AE
Sequence domains:
Histone H2B type 1-J Chains: d, h
Molecule details ›
Chains: d, h
Length: 126 amino acids
Theoretical weight: 13.94 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P06899 (Residues: 1-126; Coverage: 100%)
Gene names: H2BC11, H2BFR, HIST1H2BJ
Sequence domains: Core histone H2A/H2B/H3/H4
DNA (40-MER) Chain: 0
Molecule details ›
Chain: 0
Length: 40 nucleotides
Theoretical weight: 12.31 KDa
DNA (40-MER) Chain: 1
Molecule details ›
Chain: 1
Length: 40 nucleotides
Theoretical weight: 12.32 KDa
DNA (218-MER) Chain: N
Molecule details ›
Chain: N
Length: 228 nucleotides
Theoretical weight: 70.59 KDa
DNA (218-MER) Chain: T
Molecule details ›
Chain: T
Length: 228 nucleotides
Theoretical weight: 70.19 KDa
RNA (5'-R(P*CP*CP*UP*GP*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*UP*G)-3') Chain: P
Molecule details ›
Chain: P
Length: 16 nucleotides
Theoretical weight: 5.12 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: 5.7Å
Relevant EMDB volumes: EMD-36251
Expression system: Escherichia coli

Quick links

Citations

1 mention without citation

Cryo-EM structures of RNA polymerase II-nucleosome complexes rewrapping transcribed DNA.
Akatsu et al. (2023)