› 7z30

Electron Microscopy
2.9Å resolution

Structure of yeast RNA Polymerase III-Ty1 integrase complex at 2.9 A (focus subunit C11 terminal Zn-ribbon in the funnel pore).

Released:
DOI: 10.2210/pdb7z30/pdb
PDB entry 7z30 coloured by chain, front view.
PDB entry 7z30 coloured by chain, side view.
PDB entry 7z30 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Structural basis of Ty1 integrase tethering to RNA polymerase III for targeted retrotransposon integration.
Nguyen PQ, Huecas S, Asif-Laidin A, Plaza-Pegueroles A, Capuzzi B, Palmic N, Conesa C, Acker J, Reguera J, Lesage P, Fernández-Tornero C
OpenAccess logo Nat Commun 14 1729 (2023)
PMID: 36977686
Related structures: EMD-14469

Function and Biology Details

Reactions catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Endonucleolytic cleavage to 5'-phosphomonoester.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero nonadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-272246 (preferred)
Entry contents:
19 distinct polypeptide molecules
Macromolecules (19 distinct):
DNA-directed RNA polymerase III subunit RPC1 Chain: A
Molecule details ›
Chain: A
Length: 1460 amino acids
Theoretical weight: 162.52 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P04051 (Residues: 1-1460; Coverage: 100%)
Gene names: O3254, RPC1, RPC160, RPO31, YOR116C, YOR3254C
Sequence domains:
DNA-directed RNA polymerase III subunit RPC2 Chain: B
Molecule details ›
Chain: B
Length: 1149 amino acids
Theoretical weight: 129.63 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P22276 (Residues: 1-1149; Coverage: 100%)
Gene names: RET1, RPC128, RPC2, YOR207C
Sequence 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
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P07703 (Residues: 1-335; Coverage: 100%)
Gene names: P8283.18, RPC40, RPC5, YPR110C
Sequence domains:
DNA-directed RNA polymerase III subunit RPC9 Chain: D
Molecule details ›
Chain: D
Length: 161 amino acids
Theoretical weight: 18.62 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P47076 (Residues: 1-161; Coverage: 100%)
Gene names: J1349, RPC17, YJL011C
Sequence domains: RNA polymerase Rpb4
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
Expression system: Saccharomyces cerevisiae S288C
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 Chain: F
Molecule details ›
Chain: F
Length: 155 amino acids
Theoretical weight: 17.93 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P20435 (Residues: 1-155; Coverage: 100%)
Gene names: P9677.8, RPB6, RPO26, YPR187W
Sequence domains: RNA polymerase Rpb6
DNA-directed RNA polymerase III subunit RPC8 Chain: G
Molecule details ›
Chain: G
Length: 212 amino acids
Theoretical weight: 24.35 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P35718 (Residues: 1-212; Coverage: 100%)
Gene names: RPC25, UNF1, YKL1, YKL144C
Sequence domains:
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
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P20436 (Residues: 1-146; Coverage: 100%)
Gene names: RPB8, YOR224C, YOR50-14
Sequence domains: RNA polymerase Rpb8
DNA-directed RNA polymerase III subunit RPC10 Chain: I
Molecule details ›
Chain: I
Length: 110 amino acids
Theoretical weight: 12.53 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q04307 (Residues: 1-110; Coverage: 100%)
Gene names: RPC11, YD9609.01C, YDR045C
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
Expression system: Saccharomyces cerevisiae S288C
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 Chain: K
Molecule details ›
Chain: K
Length: 142 amino acids
Theoretical weight: 16.17 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P28000 (Residues: 1-142; Coverage: 100%)
Gene names: N1937, RPC19, YNL113W
Sequence domains: RNA polymerase Rpb3/Rpb11 dimerisation domain
DNA-directed RNA polymerases I, II, and III subunit RPABC4 Chain: L
Molecule details ›
Chain: L
Length: 70 amino acids
Theoretical weight: 7.29 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40422 (Residues: 26-70; Coverage: 64%)
Gene names: RPB12, RPC10, YHR143BW, YHR143W-A
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit
DNA-directed RNA polymerase III subunit RPC5 Chain: M
Molecule details ›
Chain: M
Length: 282 amino acids
Theoretical weight: 32.18 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P36121 (Residues: 1-282; Coverage: 100%)
Gene names: RPC37, YKR025W
Sequence domains: RPC5 protein
DNA-directed RNA polymerase III subunit RPC4 Chain: N
Molecule details ›
Chain: N
Length: 422 amino acids
Theoretical weight: 42.12 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P25441 (Residues: 195-422; Coverage: 54%)
Gene names: D1557, RPC4, RPC53, YDL150W
Sequence domains: RNA polymerase III RPC4
DNA-directed RNA polymerase III subunit RPC3 Chain: O
Molecule details ›
Chain: O
Length: 654 amino acids
Theoretical weight: 74.11 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32349 (Residues: 1-654; Coverage: 100%)
Gene names: P9677.11, RPC3, RPC82, YPR190C
Sequence domains:
DNA-directed RNA polymerase III subunit RPC6 Chain: P
Molecule details ›
Chain: P
Length: 317 amino acids
Theoretical weight: 36.17 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32910 (Residues: 1-317; Coverage: 100%)
Gene names: N2031, RPC34, YNR003C
Sequence domains: RNA polymerase Rpc34 subunit
DNA-directed RNA polymerase III subunit RPC7 Chain: Q
Molecule details ›
Chain: Q
Length: 251 amino acids
Theoretical weight: 27.75 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P17890 (Residues: 1-251; Coverage: 100%)
Gene names: ACP2, N1769, RPC31, RPC8, YNL151C
Sequence domains: DNA-directed RNA polymerase III subunit Rpc31
Integrase Chain: W
Molecule details ›
Chain: W
Length: 635 amino acids
Theoretical weight: 71.61 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q07163 (Residues: 583-1217; Coverage: 36%)
Gene names: POL, TY1B, TYB1
Sequence domains: Integrase core domain
Unknown RNA Polymerase III chain Chain: X
Molecule details ›
Chain: X
Length: 17 amino acids
Theoretical weight: 1.46 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C

Ligands and Environments

2 bound ligands:
Ligand ZN 7 x ZN
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.9Å
Relevant EMDB volumes: EMD-14469
Expression system: Saccharomyces cerevisiae S288C

Quick links

Citations

1 review citation

From parasites to partners: exploring the intricacies of host-transposon dynamics and coevolution.
Chakrabarty et al. (2023)
1 other article