› 4c2m

X-ray diffraction
2.8Å resolution

Structure of RNA polymerase I at 2.8 A resolution

Released:
DOI: 10.2210/pdb4c2m/pdb
PDB entry 4c2m coloured by chain, front view.
PDB entry 4c2m coloured by chain, side view.
PDB entry 4c2m coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
RNA polymerase I structure and transcription regulation.
Engel C, Sainsbury S, Cheung AC, Kostrewa D, Cramer P
Nature 502 650-5 (2013)
PMID: 24153182

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-139716 (preferred)
Entry contents:
14 distinct polypeptide molecules
Macromolecules (14 distinct):
DNA-directed RNA polymerases I, II, and III subunit RPABC4 Chains: 1, L
Molecule details ›
Chains: 1, 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 Chains: 2, M
Molecule details ›
Chains: 2, 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 Chains: 3, N
Molecule details ›
Chains: 3, 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
DNA-directed RNA polymerase I subunit RPA43 Chains: 4, G, O, V
Molecule details ›
Chains: 4, G, O, V
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:
DNA-directed RNA polymerase I subunit RPA190 Chains: A, P
Molecule details ›
Chains: A, P
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:
Structure domains:
DNA-directed RNA polymerase I subunit RPA135 Chains: B, Q
Molecule details ›
Chains: B, Q
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 Chains: C, R
Molecule details ›
Chains: C, R
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 Chains: D, S
Molecule details ›
Chains: D, S
Length: 137 amino acids
Theoretical weight: 14.6 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 Chains: E, T
Molecule details ›
Chains: E, T
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 Chains: F, U
Molecule details ›
Chains: F, U
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 polymerases I, II, and III subunit RPABC3 Chains: H, W
Molecule details ›
Chains: H, W
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 Chains: I, X
Molecule details ›
Chains: I, X
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 Chains: J, Y
Molecule details ›
Chains: J, Y
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 Chains: K, Z
Molecule details ›
Chains: K, Z
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

Ligands and Environments

2 bound ligands:
Ligand ZN 14 x ZN
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA, SLS BEAMLINE X06SA
Spacegroup: P1
Unit cell:
a: 122.74Å b: 139.02Å c: 209.55Å
α: 108.06° β: 95.4° γ: 93.85°
R-values:
R R work R free
0.17 0.169 0.21

Quick links

Citations

38 review citations

The contribution of co-transcriptional RNA:DNA hybrid structures to DNA damage and genome instability.
Hamperl et al. (2014)
37 more

23 mentions without citation

Coordinated Control of rRNA Processing by RNA Polymerase I.
Scull et al. (2019)
22 more