› 5xon

Electron Microscopy
3.83Å resolution

RNA Polymerase II elongation complex bound with Spt4/5 and TFIIS

Released:
DOI: 10.2210/pdb5xon/pdb
PDB entry 5xon coloured by chain, front view.
PDB entry 5xon coloured by chain, side view.
PDB entry 5xon coloured by chain, top view.
Source organism: Komagataella phaffii GS115
Primary publication:
Structure of the complete elongation complex of RNA polymerase II with basal factors.
Ehara H, Yokoyama T, Shigematsu H, Yokoyama S, Shirouzu M, Sekine SI
Science 357 921-924 (2017)
PMID: 28775211
Related structures: EMD-6747

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 octadecamer (preferred)
PDBe Complex ID:
PDB-CPX-111377 (preferred)
Entry contents:
15 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (18 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 GS115
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 GS115
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 GS115
UniProt:
  • Canonical: C4R7L2 (Residues: 1-304; Coverage: 100%)
Gene name: PAS_chr4_0344
Sequence domains:
Structure 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 GS115
UniProt:
  • Canonical: C4R2U9 (Residues: 1-186; Coverage: 100%)
Gene name: PAS_chr2-2_0104
Sequence domains: RNA polymerase Rpb4
Structure domains: Growth Hormone; Chain: A;
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 GS115
UniProt:
  • Canonical: C4R3P8 (Residues: 1-214; Coverage: 100%)
Gene name: PAS_chr3_0157
Sequence domains:
Structure 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 GS115
UniProt:
  • Canonical: C4R1V1 (Residues: 1-155; Coverage: 100%)
Gene name: PAS_chr2-2_0434
Sequence domains: RNA polymerase Rpb6
Structure domains: Eukaryotic RPB6 RNA polymerase subunit
DNA-directed RNA polymerase subunit Chain: G
Molecule details ›
Chain: G
Length: 171 amino acids
Theoretical weight: 18.8 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R9A1 (Residues: 1-171; Coverage: 100%)
Gene name: PAS_chr4_0906
Sequence domains:
Structure 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 GS115
UniProt:
  • Canonical: C4R273 (Residues: 1-145; Coverage: 100%)
Gene name: PAS_chr2-2_0309
Sequence domains: RNA polymerase Rpb8
Structure domains: Nucleic acid-binding proteins
DNA-directed RNA polymerase subunit Chain: I
Molecule details ›
Chain: I
Length: 115 amino acids
Theoretical weight: 13.61 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4QY79 (Residues: 9-113; Coverage: 93%)
Gene name: PAS_chr1-4_0359
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 GS115
UniProt:
  • Canonical: C4R009 (Residues: 1-72; Coverage: 100%)
Gene name: PAS_chr2-1_0223
Sequence domains: RNA polymerases N / 8 kDa subunit
Structure domains: Homeodomain-like
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 GS115
UniProt:
  • Canonical: C4R3Z5 (Residues: 1-118; Coverage: 100%)
Gene name: PAS_chr3_0244
Sequence domains:
Structure domains: RNA polymerase, RBP11-like subunit
RNA polymerase subunit, found in RNA polymerase complexes I, II, and III Chain: L
Molecule details ›
Chain: L
Length: 72 amino acids
Theoretical weight: 7.86 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4QWA8 (Residues: 1-69; Coverage: 95%)
Gene name: PAS_chr1-1_0166
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit
Structure domains: RNA polymerase ii, chain L
Transcription elongation factor Chain: U
Molecule details ›
Chain: U
Length: 190 amino acids
Theoretical weight: 21.69 KDa
Source organism: Komagataella phaffii GS115
Expression system: Escherichia coli
UniProt:
  • Canonical: C4R2R6 (Residues: 99-285; Coverage: 66%)
Gene name: PAS_chr2-2_0135
Sequence domains:
Transcription elongation factor SPT4 Chain: V
Molecule details ›
Chain: V
Length: 108 amino acids
Theoretical weight: 12.04 KDa
Source organism: Komagataella phaffii GS115
Expression system: Escherichia coli
UniProt:
  • Canonical: C4R0E6 (Residues: 8-114; Coverage: 94%)
Gene name: PAS_chr2-1_0350
Sequence domains: Spt4/RpoE2 zinc finger
Structure domains: Herpes Virus-1
Transcription elongation factor SPT5 Chain: W
Molecule details ›
Chain: W
Length: 612 amino acids
Theoretical weight: 68.28 KDa
Source organism: Komagataella phaffii GS115
Expression system: Escherichia coli
UniProt:
  • Canonical: C4R370 (Residues: 206-815; Coverage: 67%)
Gene name: PAS_chr3_1136
Sequence domains:
Structure domains: NusG, N-terminal domain
DNA (48-MER) Chain: T
Molecule details ›
Chain: T
Length: 48 nucleotides
Theoretical weight: 14.66 KDa
DNA (48-MER) Chain: N
Molecule details ›
Chain: N
Length: 48 nucleotides
Theoretical weight: 14.92 KDa
RNA (30-MER) Chain: P
Molecule details ›
Chain: P
Length: 30 nucleotides
Theoretical weight: 9.49 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: 3.83Å
Relevant EMDB volumes: EMD-6747
Expression system: Escherichia coli

Quick links

Citations

28 review citations

Eukaryotic core promoters and the functional basis of transcription initiation.
Haberle et al. (2018)
27 more

10 mentions without citation

Structural basis for the initiation of eukaryotic transcription-coupled DNA repair.
Xu et al. (2017)
9 more