› 5m3f

Electron Microscopy
3.8Å resolution

Yeast RNA polymerase I elongation complex at 3.8A

Released:
DOI: 10.2210/pdb5m3f/pdb
PDB entry 5m3f coloured by chain, front view.
PDB entry 5m3f coloured by chain, side view.
PDB entry 5m3f coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Structure of RNA polymerase I transcribing ribosomal DNA genes.
Neyer S, Kunz M, Geiss C, Hantsche M, Hodirnau VV, Seybert A, Engel C, Scheffer MP, Cramer P, Frangakis AS
Nature 540 607-610 (2016)
PMID: 27842382
Related structures: EMD-4147

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 heptadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119006 (preferred)
Entry contents:
14 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (17 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 S288C
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 S288C
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 S288C
UniProt:
  • Canonical: P07703 (Residues: 1-335; Coverage: 100%)
Gene names: P8283.18, RPC40, RPC5, YPR110C
Sequence domains:
Structure domains:
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 S288C
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 S288C
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 Chain: H
Molecule details ›
Chain: H
Length: 146 amino acids
Theoretical weight: 16.53 KDa
Source organism: Saccharomyces cerevisiae S288C
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 S288C
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 S288C
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 S288C
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 S288C
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 S288C
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 S288C
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 RPA14 Chain: D
Molecule details ›
Chain: D
Length: 137 amino acids
Theoretical weight: 14.6 KDa
Source organism: Saccharomyces cerevisiae S288C
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 polymerase I subunit RPA43 Chain: G
Molecule details ›
Chain: G
Length: 326 amino acids
Theoretical weight: 36.26 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P46669 (Residues: 1-326; Coverage: 100%)
Gene names: O6271, RPA43, RRN12, YOR340C
Sequence domains:
Structure domains: Nucleic acid-binding proteins
template DNA Chain: T
Molecule details ›
Chain: T
Length: 39 nucleotides
Theoretical weight: 11.94 KDa
non-template DNA Chain: U
Molecule details ›
Chain: U
Length: 39 nucleotides
Theoretical weight: 12.09 KDa
RNA Chain: R
Molecule details ›
Chain: R
Length: 20 nucleotides
Theoretical weight: 6.38 KDa

Ligands and Environments

3 bound ligands:
Ligand ZN 6 x ZN
Ligand MG 1 x MG
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.8Å
Relevant EMDB volumes: EMD-4147

Quick links

Citations

22 review citations

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

5 mentions without citation

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