› 6kf4

Electron Microscopy
3.97Å resolution

Cryo-EM structure of Thermococcus kodakarensis RNA polymerase

Released:
DOI: 10.2210/pdb6kf4/pdb
PDB entry 6kf4 coloured by chain, front view.
PDB entry 6kf4 coloured by chain, side view.
PDB entry 6kf4 coloured by chain, top view.
Source organism: Thermococcus kodakarensis KOD1
Primary publication:
Direct binding of TFEα opens DNA binding cleft of RNA polymerase.
Jun SH, Hyun J, Cha JS, Kim H, Bartlett MS, Cho HS, Murakami KS
Nat Commun 11 6123 (2020)
PMID: 33257704
Related structures: EMD-9969, EMD-9961

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 dodecamer (preferred)
PDBe Complex ID:
PDB-CPX-177269 (preferred)
Entry contents:
12 distinct polypeptide molecules
Macromolecules (12 distinct):
DNA-directed RNA polymerase subunit Rpo1N Chain: A
Molecule details ›
Chain: A
Length: 906 amino acids
Theoretical weight: 103.04 KDa
Source organism: Thermococcus kodakarensis KOD1
UniProt:
  • Canonical: Q5JE33 (Residues: 1-906; Coverage: 100%)
Gene names: TK1082, rpo1N, rpoA1
Sequence domains:
DNA-directed RNA polymerase subunit beta Chain: B
Molecule details ›
Chain: B
Length: 1123 amino acids
Theoretical weight: 127.47 KDa
Source organism: Thermococcus kodakarensis KOD1
UniProt:
  • Canonical: Q5JE32 (Residues: 1-1123; Coverage: 100%)
Gene name: TK1083
Sequence domains:
DNA-directed RNA polymerase subunit Rpo1C Chain: C
Molecule details ›
Chain: C
Length: 391 amino acids
Theoretical weight: 43.73 KDa
Source organism: Thermococcus kodakarensis KOD1
UniProt:
  • Canonical: Q5JE34 (Residues: 1-391; Coverage: 100%)
Gene names: TK1081, rpo1C, rpoA2
Sequence domains: RNA polymerase Rpb1, domain 5
DNA-directed RNA polymerase subunit Rpo3 Chain: D
Molecule details ›
Chain: D
Length: 259 amino acids
Theoretical weight: 29.43 KDa
Source organism: Thermococcus kodakarensis KOD1
UniProt:
  • Canonical: Q5JJF4 (Residues: 1-259; Coverage: 100%)
Gene names: TK1503, rpo3, rpoD
Sequence domains:
DNA-directed RNA polymerase subunit Rpo7 Chain: E
Molecule details ›
Chain: E
Length: 190 amino acids
Theoretical weight: 21.89 KDa
Source organism: Thermococcus kodakarensis KOD1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5JIY4 (Residues: 1-190; Coverage: 100%)
Gene names: TK1699, rpo7, rpoE
Sequence domains:
DNA-directed RNA polymerase subunit Rpo4 Chain: F
Molecule details ›
Chain: F
Length: 122 amino acids
Theoretical weight: 14.52 KDa
Source organism: Thermococcus kodakarensis KOD1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5JI52 (Residues: 1-114; Coverage: 99%)
Gene names: TK0901, rpo4, rpoF
Sequence domains: RNA polymerase Rpb4
DNA-directed RNA polymerase subunit Rpo5 Chain: H
Molecule details ›
Chain: H
Length: 82 amino acids
Theoretical weight: 9.52 KDa
Source organism: Thermococcus kodakarensis KOD1
UniProt:
  • Canonical: Q5JE31 (Residues: 1-82; Coverage: 100%)
Gene names: TK1084, rpo5, rpoH
Sequence domains: RNA polymerase Rpb5, C-terminal domain
DNA-directed RNA polymerase subunit Rpo6 Chain: K
Molecule details ›
Chain: K
Length: 57 amino acids
Theoretical weight: 6.29 KDa
Source organism: Thermococcus kodakarensis KOD1
UniProt:
  • Canonical: Q5JJD0 (Residues: 1-57; Coverage: 100%)
Gene names: TK1498, rpo6, rpoK
Sequence domains: RNA polymerase Rpb6
DNA-directed RNA polymerase subunit Rpo11 Chain: L
Molecule details ›
Chain: L
Length: 94 amino acids
Theoretical weight: 11.01 KDa
Source organism: Thermococcus kodakarensis KOD1
UniProt:
  • Canonical: Q5JE88 (Residues: 1-94; Coverage: 100%)
Gene names: TK1167, rpo11, rpoL
Sequence domains:
DNA-directed RNA polymerase subunit Rpo10 Chain: N
Molecule details ›
Chain: N
Length: 65 amino acids
Theoretical weight: 7.6 KDa
Source organism: Thermococcus kodakarensis KOD1
UniProt:
  • Canonical: Q5JJC9 (Residues: 1-65; Coverage: 100%)
Gene names: TK1499, rpo10, rpoN
Sequence domains: RNA polymerases N / 8 kDa subunit
DNA-directed RNA polymerase subunit Rpo12 Chain: P
Molecule details ›
Chain: P
Length: 49 amino acids
Theoretical weight: 5.55 KDa
Source organism: Thermococcus kodakarensis KOD1
UniProt:
  • Canonical: Q5JDM8 (Residues: 1-49; Coverage: 100%)
Gene names: TK0616, rpo12, rpoP
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit
Transcription factor E Chain: G
Molecule details ›
Chain: G
Length: 185 amino acids
Theoretical weight: 22.09 KDa
Source organism: Thermococcus kodakarensis KOD1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5JDD5 (Residues: 1-185; Coverage: 100%)
Gene names: TK2024, tfe
Sequence domains: TFIIE alpha subunit

Ligands and Environments

2 bound ligands:
Ligand MG 1 x MG
Ligand ZN 6 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.97Å
Relevant EMDB volumes: EMD-9961, EMD-9969
Expression system: Escherichia coli

Quick links

Citations

2 citation in other articles

Structural basis of RNA polymerase inhibition by viral and host factors.
Pilotto et al. (2021)
1 more