3hkz

X-ray diffraction
3.4Å resolution

The X-ray crystal structure of RNA polymerase from Archaea

Released:
Primary publication:
The X-ray crystal structure of RNA polymerase from Archaea.
Nature 451 851-4 (2008)
PMID: 18235446

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero tridecamer (preferred)
Entry contents:
13 distinct polypeptide molecules
Macromolecules (13 distinct):
DNA-directed RNA polymerase subunit A'' Chains: C, M
Molecule details ›
Chains: C, M
Length: 395 amino acids
Theoretical weight: 43.87 KDa
Source organism: Saccharolobus solfataricus P2
UniProt:
  • Canonical: P58192 (Residues: 1-392; Coverage: 100%)
Gene names: SSO0223, rpoA2
Sequence domains: RNA polymerase Rpb1, domain 5
Structure domains: DNA polymerase; domain 1
DNA-directed RNA polymerase subunit D Chains: D, O
Molecule details ›
Chains: D, O
Length: 265 amino acids
Theoretical weight: 30.33 KDa
Source organism: Saccharolobus solfataricus P2
UniProt:
  • Canonical: P95989 (Residues: 1-265; Coverage: 100%)
Gene names: C04_051, SSO0071, rpoD
Sequence domains:
Structure domains:
S1 motif domain-containing protein Chains: E, Q
Molecule details ›
Chains: E, Q
Length: 180 amino acids
Theoretical weight: 20.35 KDa
Source organism: Saccharolobus solfataricus P2
UniProt:
  • Canonical: Q980A3 (Residues: 1-180; Coverage: 100%)
Gene names: SSO0415, rpoE1
Sequence domains:
Structure domains:
DNA-directed RNA polymerase subunit F Chains: F, R
Molecule details ›
Chains: F, R
Length: 113 amino acids
Theoretical weight: 12.83 KDa
Source organism: Saccharolobus solfataricus P2
UniProt:
  • Canonical: Q9UXD9 (Residues: 1-113; Coverage: 100%)
Gene names: HFC64_15350, ORF-c20_042, SSOP1_0775, SULA_1833, SULB_1834, SULC_1832, SULG_09200, SULH_09200, SULI_09200, SULM_09190, SULN_09190, SULO_09200, SULZ_09125
Sequence domains: RNA polymerase Rpb4
Structure domains:
DNA-directed RNA polymerase, subunit G (RpoG) Chains: G, S
Molecule details ›
Chains: G, S
Length: 132 amino acids
Theoretical weight: 14.99 KDa
Source organism: Saccharolobus solfataricus P2
UniProt:
  • Canonical: Q980L5 (Residues: 1-132; Coverage: 100%)
Gene names: SSO0277, rpoG
Sequence domains: DNA-directed RNA polymerase, subunit G
Structure domains: Nucleic acid-binding proteins
DNA-directed RNA polymerase subunit H Chains: H, T
Molecule details ›
Chains: H, T
Length: 84 amino acids
Theoretical weight: 9.69 KDa
Source organism: Saccharolobus solfataricus P2
UniProt:
  • Canonical: Q980Q9 (Residues: 1-84; Coverage: 100%)
Gene names: SSO5468, rpoH
Sequence domains: RNA polymerase Rpb5, C-terminal domain
Structure domains: RPB5-like RNA polymerase subunit
DNA-directed RNA polymerase subunit K Chains: K, U
Molecule details ›
Chains: K, U
Length: 95 amino acids
Theoretical weight: 10.87 KDa
Source organism: Saccharolobus solfataricus P2
UniProt:
  • Canonical: Q97ZJ9 (Residues: 1-95; Coverage: 100%)
Gene names: SSO6768, rpoK
Sequence domains: RNA polymerase Rpb6
Structure domains: Eukaryotic RPB6 RNA polymerase subunit
DNA-directed RNA polymerase subunit L Chains: L, V
Molecule details ›
Chains: L, V
Length: 92 amino acids
Theoretical weight: 10.3 KDa
Source organism: Saccharolobus solfataricus P2
UniProt:
  • Canonical: Q980K0 (Residues: 1-92; Coverage: 100%)
Gene names: SSO5577, rpoL
Sequence domains: RNA polymerase Rpb3/Rpb11 dimerisation domain
Structure domains: RNA polymerase, RBP11-like subunit
DNA-directed RNA polymerase subunit N Chains: N, W
Molecule details ›
Chains: N, W
Length: 66 amino acids
Theoretical weight: 7.6 KDa
Source organism: Saccharolobus solfataricus P2
UniProt:
  • Canonical: Q980Z8 (Residues: 1-66; Coverage: 100%)
Gene names: SSO5140, rpoN
Sequence domains: RNA polymerases N / 8 kDa subunit
Structure domains: Homeodomain-like
DNA-directed RNA polymerase subunit P Chains: P, X
Molecule details ›
Chains: P, X
Length: 48 amino acids
Theoretical weight: 5.61 KDa
Source organism: Saccharolobus solfataricus P2
UniProt:
  • Canonical: Q97ZX7 (Residues: 1-48; Coverage: 100%)
Gene names: SSO5865, rpoP
Structure domains: RNA polymerase ii, chain L
RNA_pol_Rpo13 domain-containing protein Chains: Y, Z
Molecule details ›
Chains: Y, Z
Length: 104 amino acids
Theoretical weight: 12.2 KDa
Source organism: Saccharolobus solfataricus P2
UniProt:
  • Canonical: Q980B8 (Residues: 1-104; Coverage: 100%)
Gene name: SSO0396
Sequence domains: RNA polymerase Rpo13 subunit HTH domain
Structure domains: DNA Excision Repair, Uvrb; Chain A

Ligands and Environments

3 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P21
Unit cell:
a: 125.82Å b: 201.235Å c: 196.05Å
α: 90° β: 100.92° γ: 90°
R-values:
R R work R free
0.269 0.265 0.341