› 7xtd

Electron Microscopy
3.9Å resolution

RNA polymerase II elongation complex transcribing a nucleosome (EC58oct)

Released:
DOI: 10.2210/pdb7xtd/pdb
PDB entry 7xtd coloured by chain, front view.
PDB entry 7xtd coloured by chain, side view.
PDB entry 7xtd coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of nucleosome disassembly and reassembly by RNAPII elongation complex with FACT.
Ehara H, Kujirai T, Shirouzu M, Kurumizaka H, Sekine SI
Science eabp9466 (2022)
PMID: 35981082
Related structures: EMD-33447

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 35-mer (preferred)
PDBe Complex ID:
PDB-CPX-111381 (preferred)
Entry contents:
28 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (31 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:
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: 911 amino acids
Theoretical weight: 101.46 KDa
Source organism: Komagataella phaffii
Expression system: Escherichia coli
UniProt:
  • Canonical: C4R370 (Residues: 1-908; Coverage: 100%)
Gene name: PAS_chr3_1136
Sequence domains:
Transcription elongation factor Spt6 Chain: m
Molecule details ›
Chain: m
Length: 1503 amino acids
Theoretical weight: 173.24 KDa
Source organism: Komagataella phaffii
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: C4R7H2 (Residues: 1-1500; Coverage: 100%)
Gene name: PAS_chr4_0308
Sequence domains:
TFIIS N-terminal domain-containing protein Chain: n
Molecule details ›
Chain: n
Length: 417 amino acids
Theoretical weight: 46.91 KDa
Source organism: Komagataella phaffii
Expression system: Escherichia coli
UniProt:
  • Canonical: C4R7L8 (Residues: 1-414; Coverage: 100%)
Gene name: PAS_chr4_0349
Sequence domains: TFIIS helical bundle-like domain
Component of the Paf1p complex Chain: q
Molecule details ›
Chain: q
Length: 1084 amino acids
Theoretical weight: 124.98 KDa
Source organism: Komagataella phaffii
Expression system: Escherichia coli
UniProt:
  • Canonical: C4R6B2 (Residues: 1-1044; Coverage: 100%)
Gene name: PAS_chr3_1035
Sequence domains: Tetratricopeptide repeat
Plus3 domain-containing protein Chain: r
Molecule details ›
Chain: r
Length: 544 amino acids
Theoretical weight: 62.3 KDa
Source organism: Komagataella phaffii
Expression system: Escherichia coli
UniProt:
  • Canonical: F2QQ42 (Residues: 1-514; Coverage: 100%)
Gene names: PP7435_Chr1-1405, RTF1
Sequence domains: Plus-3 domain
RNA polymerase-associated protein LEO1 Chain: u
Molecule details ›
Chain: u
Length: 459 amino acids
Theoretical weight: 52.39 KDa
Source organism: Komagataella phaffii
Expression system: Escherichia coli
UniProt:
  • Canonical: C4R3K1 (Residues: 1-429; Coverage: 100%)
Gene name: PAS_chr3_1154
Sequence domains: Leo1-like protein
RNAP II-associated protein Chain: v
Molecule details ›
Chain: v
Length: 396 amino acids
Theoretical weight: 46.05 KDa
Source organism: Komagataella phaffii
Expression system: Escherichia coli
UniProt:
  • Canonical: C4R997 (Residues: 1-393; Coverage: 100%)
Gene name: PAS_chr4_0902
Sequence domains: Paf1
Cell division control protein 73 C-terminal domain-containing protein Chain: x
Molecule details ›
Chain: x
Length: 395 amino acids
Theoretical weight: 44.76 KDa
Source organism: Komagataella phaffii
Expression system: Escherichia coli
UniProt:
  • Canonical: C4R1E6 (Residues: 1-365; Coverage: 100%)
Gene name: PAS_chr2-1_0674
Sequence domains: RNA pol II accessory factor, Cdc73 family, C-terminal
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: 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: 133 amino acids
Theoretical weight: 14.45 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: 129 amino acids
Theoretical weight: 14.22 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
FACT complex subunit Chain: j
Molecule details ›
Chain: j
Length: 1008 amino acids
Theoretical weight: 115.22 KDa
Source organism: Komagataella phaffii
Expression system: Escherichia coli
UniProt:
  • Canonical: C4QYQ8 (Residues: 1-1005; Coverage: 100%)
Gene name: PAS_chr1-4_0529
Sequence domains:
FACT complex subunit POB3 Chain: k
Molecule details ›
Chain: k
Length: 531 amino acids
Theoretical weight: 60.29 KDa
Source organism: Komagataella phaffii
Expression system: Escherichia coli
UniProt:
  • Canonical: F2QNN8 (Residues: 32-559; Coverage: 95%)
Gene names: POB3, PP7435_Chr1-0311
Sequence domains:
DNA (198-MER) Chain: N
Molecule details ›
Chain: N
Length: 198 nucleotides
Theoretical weight: 61.38 KDa
DNA (198-MER) Chain: T
Molecule details ›
Chain: T
Length: 198 nucleotides
Theoretical weight: 60.87 KDa
RNA (5'-R(P*UP*GP*UP*AP*AP*UP*CP*CP*CP*CP*UP*UP*GP*GP*CP*GP*GP*UP*U)-3') Chain: P
Molecule details ›
Chain: P
Length: 19 nucleotides
Theoretical weight: 6.01 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: 3.9Å
Relevant EMDB volumes: EMD-33447
Expression systems:
  • Escherichia coli
  • Spodoptera frugiperda

Quick links

Citations

4 review citations

The TFIIS N-terminal domain (TND): a transcription assembly module at the interface of order and disorder.
Cermakova et al. (2023)
3 more

1 mention without citation

Structural Transition of the Nucleosome during Transcription Elongation.
Kujirai et al. (2023)