› 4v8s

X-ray diffraction
4.32Å resolution

Archaeal RNAP-DNA binary complex at 4.32Ang

Released:
DOI: 10.2210/pdb4v8s/pdb
PDB entry 4v8s coloured by chain, front view.
PDB entry 4v8s coloured by chain, side view.
PDB entry 4v8s coloured by chain, top view.
Source organism: Saccharolobus shibatae B12
Primary publication:
Structural and functional analyses of the interaction of archaeal RNA polymerase with DNA.
Wojtas MN, Mogni M, Millet O, Bell SD, Abrescia NG
Nucleic Acids Res 40 9941-52 (2012)
PMID: 22848102

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 pentadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-110788 (preferred)
Entry contents:
13 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (15 distinct):
DNA-directed RNA polymerase subunit Rpo6 Chains: AI, BK
Molecule details ›
Chains: AI, BK
Length: 95 amino acids
Theoretical weight: 10.73 KDa
Source organism: Saccharolobus shibatae B12
UniProt:
  • Canonical: B8YB61 (Residues: 1-95; Coverage: 100%)
Gene names: J5U23_02568, rpo6, rpoK
Sequence domains: RNA polymerase Rpb6
DNA-directed RNA polymerase subunit Rpo13 Chains: AJ, BQ
Molecule details ›
Chains: AJ, BQ
Length: 104 amino acids
Theoretical weight: 12.17 KDa
Source organism: Saccharolobus shibatae B12
UniProt:
  • Canonical: B8YB65 (Residues: 1-104; Coverage: 100%)
Gene names: J5U23_03039, rpo13
Sequence domains: RNA polymerase Rpo13 subunit HTH domain
DNA-directed RNA polymerase subunit Rpo11 Chains: AM, BL
Molecule details ›
Chains: AM, BL
Length: 92 amino acids
Theoretical weight: 10.21 KDa
Source organism: Saccharolobus shibatae B12
UniProt:
  • Canonical: B8YB62 (Residues: 1-92; Coverage: 100%)
Gene names: J5U23_03144, rpo11, rpoL
Sequence domains:
DNA-directed RNA polymerase subunit Rpo10 Chains: AO, BN
Molecule details ›
Chains: AO, BN
Length: 66 amino acids
Theoretical weight: 7.62 KDa
Source organism: Saccharolobus shibatae B12
UniProt:
  • Canonical: B8YB63 (Residues: 1-66; Coverage: 100%)
Gene names: J5U23_00180, rpo10, rpoN
Sequence domains: RNA polymerases N / 8 kDa subunit
DNA-directed RNA polymerase subunit Rpo2 Chains: AR, BB
Molecule details ›
Chains: AR, BB
Length: 1131 amino acids
Theoretical weight: 127.58 KDa
Source organism: Saccharolobus shibatae B12
UniProt:
  • Canonical: B8YB55 (Residues: 1-1128; Coverage: 100%)
Gene names: J5U23_00030, rpo2
Sequence domains:
DNA-directed RNA polymerase subunit Rpo3 Chains: AS, BD
Molecule details ›
Chains: AS, BD
Length: 265 amino acids
Theoretical weight: 30.18 KDa
Source organism: Saccharolobus shibatae B12
UniProt:
  • Canonical: B8YB56 (Residues: 1-265; Coverage: 100%)
Gene names: J5U23_00176, rpo3, rpoD
Sequence domains:
DNA-directed RNA polymerase subunit Rpo7 Chains: AT, BE
Molecule details ›
Chains: AT, BE
Length: 180 amino acids
Theoretical weight: 20.33 KDa
Source organism: Saccharolobus shibatae B12
UniProt:
  • Canonical: B8YB57 (Residues: 1-180; Coverage: 100%)
Gene names: J5U23_03022, rpo7, rpoE
Sequence domains:
DNA-directed RNA polymerase subunit Rpo4 Chains: AU, BF
Molecule details ›
Chains: AU, BF
Length: 113 amino acids
Theoretical weight: 12.82 KDa
Source organism: Saccharolobus shibatae B12
UniProt:
  • Canonical: B8YB58 (Residues: 1-113; Coverage: 100%)
Gene names: J5U23_02661, rpo4, rpoF
Sequence domains: RNA polymerase Rpb4
DNA-directed RNA polymerase subunit Rpo8 Chains: AV, BG
Molecule details ›
Chains: AV, BG
Length: 132 amino acids
Theoretical weight: 15.14 KDa
Source organism: Saccharolobus shibatae B12
UniProt:
  • Canonical: B8YB59 (Residues: 1-131; Coverage: 100%)
Gene names: J5U23_03191, rpo8, rpoG
Sequence domains: DNA-directed RNA polymerase, subunit G
DNA-directed RNA polymerase subunit Rpo1N Chains: AW, BA
Molecule details ›
Chains: AW, BA
Length: 880 amino acids
Theoretical weight: 99.77 KDa
Source organism: Saccharolobus shibatae B12
UniProt:
  • Canonical: B8YB53 (Residues: 1-880; Coverage: 100%)
Gene names: J5U23_00031, rpo1N, rpoA1
Sequence domains:
DNA-directed RNA polymerase subunit Rpo12 Chains: AX, BP
Molecule details ›
Chains: AX, BP
Length: 48 amino acids
Theoretical weight: 5.61 KDa
Source organism: Saccharolobus shibatae B12
UniProt:
  • Canonical: B8YB64 (Residues: 1-48; Coverage: 100%)
Gene names: J5U23_02993, rpo12, rpoP
DNA-directed RNA polymerase subunit Rpo1C Chains: AY, BC
Molecule details ›
Chains: AY, BC
Length: 395 amino acids
Theoretical weight: 43.79 KDa
Source organism: Saccharolobus shibatae B12
UniProt:
  • Canonical: B8YB54 (Residues: 1-392; Coverage: 100%)
Gene names: J5U23_00032, rpo1C, rpoA2
Sequence domains: RNA polymerase Rpb1, domain 5
DNA-directed RNA polymerase subunit Rpo5 Chains: AZ, BH
Molecule details ›
Chains: AZ, BH
Length: 84 amino acids
Theoretical weight: 9.69 KDa
Source organism: Saccharolobus shibatae B12
UniProt:
  • Canonical: B8YB60 (Residues: 1-84; Coverage: 100%)
Gene names: J5U23_00029, rpo5, rpoH
Sequence domains: RNA polymerase Rpb5, C-terminal domain
5'-D(*TP*CP*TP*TP*AP*TP*AP*CP*TP*CP*TP*AP*TP*CP)-3' Chains: AC, BR
Molecule details ›
Chains: AC, BR
Length: 14 nucleotides
Theoretical weight: 4.18 KDa
5'-D(*AP*TP*AP*GP*AP*GP*TP*AP*TP*AP*AP*GP*AP*TP *AP*G)-3' Chains: AD, BS
Molecule details ›
Chains: AD, BS
Length: 16 nucleotides
Theoretical weight: 4.99 KDa

Ligands and Environments

3 bound ligands:
Ligand ZN 12 x ZN
Ligand SF4 2 x SF4
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM14
Spacegroup: P21
Unit cell:
a: 134.134Å b: 199.416Å c: 214.246Å
α: 90° β: 103.54° γ: 90°
R-values:
R R work R free
0.293 0.292 0.31

Quick links

Citations

5 review citations

Molecular Mechanisms of Transcription Initiation-Structure, Function, and Evolution of TFE/TFIIE-Like Factors and Open Complex Formation.
Blombach et al. (2016)
4 more

3 mentions without citation

RNA Polymerase Accommodates a Pause RNA Hairpin by Global Conformational Rearrangements that Prolong Pausing.
Kang et al. (2018)
2 more