› 9bcu

Electron Microscopy
2.2Å resolution

Cryo-EM structure of Thermococcus kodakarensis FttA-dependent transcription pre-termination complex containing 52 nt RNA

Released:
DOI: 10.2210/pdb9bcu/pdb
PDB entry 9bcu coloured by chain, front view.
PDB entry 9bcu coloured by chain, side view.
PDB entry 9bcu coloured by chain, top view.
Source organism: Thermococcus kodakarensis
Primary publication:
Structural basis of archaeal FttA-dependent transcription termination.
You L, Wang C, Molodtsov V, Kuznedelov K, Miao X, Wenck BR, Ulisse P, Sanders TJ, Marshall CJ, Firlar E, Kaelber JT, Santangelo TJ, Ebright RH
Nature (2024)
PMID: 39322680
Related structures: EMD-44439

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 octadecamer (preferred)
PDBe Complex ID:
PDB-CPX-275889 (preferred)
Entry contents:
14 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (17 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
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
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
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: 261 amino acids
Theoretical weight: 29.66 KDa
Source organism: Thermococcus kodakarensis
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
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
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
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: 60 amino acids
Theoretical weight: 6.58 KDa
Source organism: Thermococcus kodakarensis
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
UniProt:
  • Canonical: Q5JE88 (Residues: 1-94; Coverage: 100%)
Gene names: TK1167, rpo11, rpoL
Sequence domains: RNA polymerase Rpb3/Rpb11 dimerisation domain
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
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
UniProt:
  • Canonical: Q5JDM8 (Residues: 1-49; Coverage: 100%)
Gene names: TK0616, rpo12, rpoP
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit
Transcription elongation factor Spt5 Chain: G
Molecule details ›
Chain: G
Length: 152 amino acids
Theoretical weight: 16.78 KDa
Source organism: Thermococcus kodakarensis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5JH33 (Residues: 1-152; Coverage: 100%)
Gene names: TK1419, spt5
Sequence domains:
Transcription elongation factor Spt4 Chain: I
Molecule details ›
Chain: I
Length: 73 amino acids
Theoretical weight: 8.56 KDa
Source organism: Thermococcus kodakarensis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5JIY5 (Residues: 1-67; Coverage: 100%)
Gene names: TK1698, spt4
Sequence domains: Spt4/RpoE2 zinc finger
Transcription termination factor FttA Chains: J, M
Molecule details ›
Chains: J, M
Length: 648 amino acids
Theoretical weight: 73.47 KDa
Source organism: Thermococcus kodakarensis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5JH24 (Residues: 1-648; Coverage: 100%)
Gene names: TK1428, fttA
Sequence domains:
non-template strand DNA Chain: 5
Molecule details ›
Chain: 5
Length: 36 nucleotides
Theoretical weight: 11.1 KDa
template strand DNA Chain: 6
Molecule details ›
Chain: 6
Length: 36 nucleotides
Theoretical weight: 11.06 KDa
RNA (29-MER) Chain: 7
Molecule details ›
Chain: 7
Length: 52 nucleotides
Theoretical weight: 16.03 KDa

Ligands and Environments

2 bound ligands:
Ligand MG 1 x MG
Ligand ZN 8 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.2Å
Relevant EMDB volumes: EMD-44439
Expression system: Escherichia coli

Quick links