› 4c3h

X-ray diffraction
3.27Å resolution

Structure of 14-subunit RNA polymerase I at 3.27 A resolution, crystal form C2-93

Released:
DOI: 10.2210/pdb4c3h/pdb
PDB entry 4c3h coloured by chain, front view.
PDB entry 4c3h coloured by chain, side view.
PDB entry 4c3h coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Crystal structure of the 14-subunit RNA polymerase I.
Fernández-Tornero C, Moreno-Morcillo M, Rashid UJ, Taylor NM, Ruiz FM, Gruene T, Legrand P, Steuerwald U, Müller CW
Nature 502 644-9 (2013)
PMID: 24153184

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 tetradecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139714 (preferred)
Entry contents:
14 distinct polypeptide molecules
Macromolecules (14 distinct):
DNA-directed RNA polymerase I subunit RPA190 Chain: A
Molecule details ›
Chain: A
Length: 1664 amino acids
Theoretical weight: 186.68 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P10964 (Residues: 1-1664; Coverage: 100%)
Gene names: O6276, RPA1, RPA190, RRN1, YOR341W
Sequence domains:
DNA-directed RNA polymerase I subunit RPA135 Chain: B
Molecule details ›
Chain: B
Length: 1203 amino acids
Theoretical weight: 135.91 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P22138 (Residues: 1-1203; Coverage: 100%)
Gene names: RPA135, RPA2, RRN2, SRP3, YP9531.03C, YPR010C
Sequence domains:
Structure domains:
DNA-directed RNA polymerases I and III subunit RPAC1 Chain: C
Molecule details ›
Chain: C
Length: 335 amino acids
Theoretical weight: 37.73 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P07703 (Residues: 1-335; Coverage: 100%)
Gene names: P8283.18, RPC40, RPC5, YPR110C
Sequence domains:
Structure domains:
DNA-directed RNA polymerase I subunit RPA14 Chain: D
Molecule details ›
Chain: D
Length: 137 amino acids
Theoretical weight: 14.59 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P50106 (Residues: 1-137; Coverage: 100%)
Gene names: RPA14, YD8358.11, YDR156W
Sequence domains: Yeast RNA polymerase I subunit RPA14
Structure domains: Single alpha-helices involved in coiled-coils or other helix-helix interfaces
DNA-directed RNA polymerases I, II, and III subunit RPABC1 Chain: E
Molecule details ›
Chain: E
Length: 215 amino acids
Theoretical weight: 25.12 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P20434 (Residues: 1-215; Coverage: 100%)
Gene names: RPA7, RPB5, RPC9, YBR1204, YBR154C
Sequence domains:
Structure domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC2 Chain: F
Molecule details ›
Chain: F
Length: 155 amino acids
Theoretical weight: 17.93 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P20435 (Residues: 1-155; Coverage: 100%)
Gene names: P9677.8, RPB6, RPO26, YPR187W
Sequence domains: RNA polymerase Rpb6
Structure domains: Eukaryotic RPB6 RNA polymerase subunit
DNA-directed RNA polymerase I subunit RPA43 Chain: G
Molecule details ›
Chain: G
Length: 326 amino acids
Theoretical weight: 36.26 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P46669 (Residues: 1-326; Coverage: 100%)
Gene names: O6271, RPA43, RRN12, YOR340C
Sequence domains:
Structure domains: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
DNA-directed RNA polymerases I, II, and III subunit RPABC3 Chain: H
Molecule details ›
Chain: H
Length: 146 amino acids
Theoretical weight: 16.53 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P20436 (Residues: 1-146; Coverage: 100%)
Gene names: RPB8, YOR224C, YOR50-14
Sequence domains: RNA polymerase Rpb8
Structure domains: Nucleic acid-binding proteins
DNA-directed RNA polymerase I subunit RPA12 Chain: I
Molecule details ›
Chain: I
Length: 125 amino acids
Theoretical weight: 13.68 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32529 (Residues: 1-125; Coverage: 100%)
Gene names: J1747, RPA12, RRN4, YJR063W
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC5 Chain: J
Molecule details ›
Chain: J
Length: 70 amino acids
Theoretical weight: 8.29 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P22139 (Residues: 1-70; Coverage: 100%)
Gene names: RPB10, YOR210W
Sequence domains: RNA polymerases N / 8 kDa subunit
Structure domains: Homeodomain-like
DNA-directed RNA polymerases I and III subunit RPAC2 Chain: K
Molecule details ›
Chain: K
Length: 142 amino acids
Theoretical weight: 16.17 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P28000 (Residues: 1-142; Coverage: 100%)
Gene names: N1937, RPC19, YNL113W
Sequence domains:
Structure domains: RNA polymerase, RBP11-like subunit
DNA-directed RNA polymerases I, II, and III subunit RPABC4 Chain: L
Molecule details ›
Chain: L
Length: 70 amino acids
Theoretical weight: 7.73 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40422 (Residues: 1-70; Coverage: 100%)
Gene names: RPB12, RPC10, YHR143BW, YHR143W-A
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit
Structure domains: RNA polymerase ii, chain L
DNA-directed RNA polymerase I subunit RPA49 Chain: M
Molecule details ›
Chain: M
Length: 415 amino acids
Theoretical weight: 46.72 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q01080 (Residues: 1-415; Coverage: 100%)
Gene names: N0880, RPA49, RRN13, YNL248C
Sequence domains: A49-like RNA polymerase I associated factor
DNA-directed RNA polymerase I subunit RPA34 Chain: N
Molecule details ›
Chain: N
Length: 233 amino acids
Theoretical weight: 26.93 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P47006 (Residues: 1-233; Coverage: 100%)
Gene names: J0637, RPA34, YJL148W
Sequence domains: DNA-directed RNA polymerase I subunit RPA34.5

Ligands and Environments

1 bound ligand:
Ligand ZN 7 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: C2
Unit cell:
a: 425.24Å b: 140.62Å c: 139.72Å
α: 90° β: 93.35° γ: 90°
R-values:
R R work R free
0.221 0.22 0.226

Quick links

Citations

34 review citations

Organization and regulation of gene transcription.
Cramer P. (2019)
33 more

9 mentions without citation

Functional divergence of eukaryotic RNA polymerases: unique properties of RNA polymerase I suit its cellular role.
Viktorovskaya et al. (2015)
8 more