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Structure of yeast RNA Polymerase III-Ty1 integrase complex at 2.7 A (focus subunit C11, no C11 C-terminal Zn-ribbon in the funnel pore).

Electron Microscopy
2.76Å resolution
PDB entry 7z31 coloured by chain, front view.
PDB entry 7z31 coloured by chain, side view.
PDB entry 7z31 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Assembly composition:
hetero nonadecamer (preferred)
Entry contents: 19 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: DNA-directed RNA polymerase III complex and Integrase
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Multimeric state: hetero nonadecamer
Accessible surface area: 202160.71 Å2
Buried surface area: 100631.37 Å2
Dissociation area: 514.03 Å2
Dissociation energy (ΔGdiss): 1.6 kcal/mol
Dissociation entropy (TΔSdiss): 7.06 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-228488

Macromolecules

DNA-directed RNA polymerase III subunit RPC1
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
Pfam:
InterPro:
DNA-directed RNA polymerase III subunit RPC1 in PDB entry 7z31, assembly 1, front view.
DNA-directed RNA polymerase III subunit RPC1 in PDB entry 7z31, assembly 1, side view.
DNA-directed RNA polymerase III subunit RPC1 in PDB entry 7z31, assembly 1, top view.
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DNA-directed RNA polymerase III subunit RPC2
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
Pfam:
InterPro:
DNA-directed RNA polymerase III subunit RPC2 in PDB entry 7z31, assembly 1, front view.
DNA-directed RNA polymerase III subunit RPC2 in PDB entry 7z31, assembly 1, side view.
DNA-directed RNA polymerase III subunit RPC2 in PDB entry 7z31, assembly 1, top view.
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DNA-directed RNA polymerases I and III subunit RPAC1
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
Pfam:
InterPro:
DNA-directed RNA polymerases I and III subunit RPAC1 in PDB entry 7z31, assembly 1, front view.
DNA-directed RNA polymerases I and III subunit RPAC1 in PDB entry 7z31, assembly 1, side view.
DNA-directed RNA polymerases I and III subunit RPAC1 in PDB entry 7z31, assembly 1, top view.
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DNA-directed RNA polymerase III subunit RPC9
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
Pfam: RNA polymerase Rpb4
InterPro:
DNA-directed RNA polymerase III subunit RPC9 in PDB entry 7z31, assembly 1, front view.
DNA-directed RNA polymerase III subunit RPC9 in PDB entry 7z31, assembly 1, side view.
DNA-directed RNA polymerase III subunit RPC9 in PDB entry 7z31, assembly 1, top view.
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DNA-directed RNA polymerases I, II, and III subunit RPABC1
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
Pfam:
InterPro:
DNA-directed RNA polymerases I, II, and III subunit RPABC1 in PDB entry 7z31, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC1 in PDB entry 7z31, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC1 in PDB entry 7z31, assembly 1, top view.
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DNA-directed RNA polymerases I, II, and III subunit RPABC2
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
Pfam: RNA polymerase Rpb6
InterPro:
DNA-directed RNA polymerases I, II, and III subunit RPABC2 in PDB entry 7z31, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC2 in PDB entry 7z31, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC2 in PDB entry 7z31, assembly 1, top view.
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DNA-directed RNA polymerase III subunit RPC8
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
Pfam:
InterPro:
DNA-directed RNA polymerase III subunit RPC8 in PDB entry 7z31, assembly 1, front view.
DNA-directed RNA polymerase III subunit RPC8 in PDB entry 7z31, assembly 1, side view.
DNA-directed RNA polymerase III subunit RPC8 in PDB entry 7z31, assembly 1, top view.
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DNA-directed RNA polymerases I, II, and III subunit RPABC3
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
Pfam: RNA polymerase Rpb8
InterPro:
DNA-directed RNA polymerases I, II, and III subunit RPABC3 in PDB entry 7z31, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC3 in PDB entry 7z31, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC3 in PDB entry 7z31, assembly 1, top view.
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DNA-directed RNA polymerase III subunit RPC10
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
Pfam:
InterPro:
DNA-directed RNA polymerase III subunit RPC10 in PDB entry 7z31, assembly 1, front view.
DNA-directed RNA polymerase III subunit RPC10 in PDB entry 7z31, assembly 1, side view.
DNA-directed RNA polymerase III subunit RPC10 in PDB entry 7z31, assembly 1, top view.
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DNA-directed RNA polymerases I, II, and III subunit RPABC5
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
Pfam: RNA polymerases N / 8 kDa subunit
InterPro:
DNA-directed RNA polymerases I, II, and III subunit RPABC5 in PDB entry 7z31, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC5 in PDB entry 7z31, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC5 in PDB entry 7z31, assembly 1, top view.
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DNA-directed RNA polymerases I and III subunit RPAC2
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
Pfam: RNA polymerase Rpb3/Rpb11 dimerisation domain
InterPro:
DNA-directed RNA polymerases I and III subunit RPAC2 in PDB entry 7z31, assembly 1, front view.
DNA-directed RNA polymerases I and III subunit RPAC2 in PDB entry 7z31, assembly 1, side view.
DNA-directed RNA polymerases I and III subunit RPAC2 in PDB entry 7z31, assembly 1, top view.
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DNA-directed RNA polymerases I, II, and III subunit RPABC4
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
Pfam: DNA directed RNA polymerase, 7 kDa subunit
InterPro:
DNA-directed RNA polymerases I, II, and III subunit RPABC4 in PDB entry 7z31, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC4 in PDB entry 7z31, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC4 in PDB entry 7z31, assembly 1, top view.
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DNA-directed RNA polymerase III subunit RPC5
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
Pfam: RPC5 protein
InterPro: DNA-directed RNA polymerase III subunit Rpc5
DNA-directed RNA polymerase III subunit RPC5 in PDB entry 7z31, assembly 1, front view.
DNA-directed RNA polymerase III subunit RPC5 in PDB entry 7z31, assembly 1, side view.
DNA-directed RNA polymerase III subunit RPC5 in PDB entry 7z31, assembly 1, top view.
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DNA-directed RNA polymerase III subunit RPC4
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
Pfam: RNA polymerase III RPC4
InterPro: DNA-directed RNA polymerase III subunit RPC4
DNA-directed RNA polymerase III subunit RPC4 in PDB entry 7z31, assembly 1, front view.
DNA-directed RNA polymerase III subunit RPC4 in PDB entry 7z31, assembly 1, side view.
DNA-directed RNA polymerase III subunit RPC4 in PDB entry 7z31, assembly 1, top view.
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DNA-directed RNA polymerase III subunit RPC3
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
Pfam:
InterPro:
DNA-directed RNA polymerase III subunit RPC3 in PDB entry 7z31, assembly 1, front view.
DNA-directed RNA polymerase III subunit RPC3 in PDB entry 7z31, assembly 1, side view.
DNA-directed RNA polymerase III subunit RPC3 in PDB entry 7z31, assembly 1, top view.
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DNA-directed RNA polymerase III subunit RPC6
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
Pfam: RNA polymerase Rpc34 subunit
InterPro:
DNA-directed RNA polymerase III subunit RPC6 in PDB entry 7z31, assembly 1, front view.
DNA-directed RNA polymerase III subunit RPC6 in PDB entry 7z31, assembly 1, side view.
DNA-directed RNA polymerase III subunit RPC6 in PDB entry 7z31, assembly 1, top view.
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DNA-directed RNA polymerase III subunit RPC7
Chain: Q
Length: 268 amino acids
Theoretical weight: 29.2 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
Pfam: DNA-directed RNA polymerase III subunit Rpc31
InterPro: DNA-directed RNA polymerase III, subunit Rpc31
DNA-directed RNA polymerase III subunit RPC7 in PDB entry 7z31, assembly 1, front view.
DNA-directed RNA polymerase III subunit RPC7 in PDB entry 7z31, assembly 1, side view.
DNA-directed RNA polymerase III subunit RPC7 in PDB entry 7z31, assembly 1, top view.
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Integrase
Chain: W
Length: 635 amino acids
Theoretical weight: 71.61 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q12414 (Residues: 583-1217; Coverage: 36%)
Gene names: P0729, TY1B-PL, YPL257W-B, YPLWTy1-1 POL
Pfam: Integrase core domain
InterPro:
Integrase in PDB entry 7z31, assembly 1, front view.
Integrase in PDB entry 7z31, assembly 1, side view.
Integrase in PDB entry 7z31, assembly 1, top view.
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Unknown RNA polymerase III chain
Chain: X
Length: 13 amino acids
Theoretical weight: 1.12 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
Unknown RNA polymerase III chain in PDB entry 7z31, assembly 1, front view.
Unknown RNA polymerase III chain in PDB entry 7z31, assembly 1, side view.
Unknown RNA polymerase III chain in PDB entry 7z31, assembly 1, top view.
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