› 4ym7

X-ray diffraction
5.5Å resolution

RNA polymerase I structure with an alternative dimer hinge

Released:
DOI: 10.2210/pdb4ym7/pdb
PDB entry 4ym7 coloured by chain, front view.
PDB entry 4ym7 coloured by chain, side view.
PDB entry 4ym7 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
An alternative RNA polymerase I structure reveals a dimer hinge.
Kostrewa D, Kuhn CD, Engel C, Cramer P
Acta Crystallogr D Biol Crystallogr 71 1850-5 (2015)
PMID: 26327374

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 polymerase I subunit RPA190 Chains: AA, BA, CA, DA, EA, FA
Molecule details ›
Chains: AA, BA, CA, DA, EA, FA
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 Chains: AB, BB, CB, DB, EB, FB
Molecule details ›
Chains: AB, BB, CB, DB, EB, FB
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:
DNA-directed RNA polymerases I and III subunit RPAC1 Chains: AC, BC, CC, DC, EC, FC
Molecule details ›
Chains: AC, BC, CC, DC, EC, FC
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:
DNA-directed RNA polymerase I subunit RPA14 Chains: AD, BD, CD, DD, ED, FD
Molecule details ›
Chains: AD, BD, CD, DD, ED, FD
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
DNA-directed RNA polymerases I, II, and III subunit RPABC1 Chains: AE, BE, CE, DE, EE, FE
Molecule details ›
Chains: AE, BE, CE, DE, EE, FE
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:
DNA-directed RNA polymerases I, II, and III subunit RPABC2 Chains: AF, BF, CF, DF, EF, FF
Molecule details ›
Chains: AF, BF, CF, DF, EF, FF
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
DNA-directed RNA polymerase I subunit RPA43 Chains: AG, AO, BG, BO, CG, CO, DG, DO, EG, EO, FG, FO
Molecule details ›
Chains: AG, AO, BG, BO, CG, CO, DG, DO, EG, EO, FG, FO
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:
DNA-directed RNA polymerases I, II, and III subunit RPABC3 Chains: AH, BH, CH, DH, EH, FH
Molecule details ›
Chains: AH, BH, CH, DH, EH, FH
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
DNA-directed RNA polymerase I subunit RPA12 Chains: AI, BI, CI, DI, EI, FI
Molecule details ›
Chains: AI, BI, CI, DI, EI, FI
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: AJ, BJ, CJ, DJ, EJ, FJ
Molecule details ›
Chains: AJ, BJ, CJ, DJ, EJ, FJ
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
DNA-directed RNA polymerases I and III subunit RPAC2 Chains: AK, BK, CK, DK, EK, FK
Molecule details ›
Chains: AK, BK, CK, DK, EK, FK
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:
DNA-directed RNA polymerases I, II, and III subunit RPABC4 Chains: AL, BL, CL, DL, EL, FL
Molecule details ›
Chains: AL, BL, CL, DL, EL, FL
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
DNA-directed RNA polymerase I subunit RPA49 Chains: AM, BM, CM, DM, EM, FM
Molecule details ›
Chains: AM, BM, CM, DM, EM, FM
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: AN, BN, CN, DN, EN, FN
Molecule details ›
Chains: AN, BN, CN, DN, EN, FN
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 42 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: C2
Unit cell:
a: 619.48Å b: 306.62Å c: 251.78Å
α: 90° β: 97.5° γ: 90°
R-values:
R R work R free
0.196 0.196 0.236

Quick links

Citations

3 review citations

Distinct Mechanisms of Transcription Initiation by RNA Polymerases I and II.
Engel et al. (2018)
2 more