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Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 3)

Electron Microscopy
7.6Å resolution
PDB entry 5voz coloured by chain, front view.
PDB entry 5voz coloured by chain, side view.
PDB entry 5voz coloured by chain, top view.
Source organisms:
Assembly composition:
hetero 33-mer (preferred)
Entry contents: 16 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Vacuolar ATPase
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Multimeric state: hetero 33-mer
PDBe Complex ID: PDB-CPX-147634

Macromolecules

Endonuclease PI-SceI
Chains: A, C, E
Length: 617 amino acids
Theoretical weight: 67.8 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P17255 (Residues: 1-1071; Coverage: 58%)
Gene names: CLS8, D1286, TFP1, VMA1, YDL185W
Pfam:
InterPro:
Endonuclease PI-SceI in PDB entry 5voz, assembly 1, front view.
Endonuclease PI-SceI in PDB entry 5voz, assembly 1, side view.
Endonuclease PI-SceI in PDB entry 5voz, assembly 1, top view.
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V-type proton ATPase subunit B
Chains: B, D, F
Length: 517 amino acids
Theoretical weight: 57.82 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P16140 (Residues: 1-517; Coverage: 100%)
Gene names: VAT2, VMA2, YBR1002, YBR127C
Pfam:
InterPro:
V-type proton ATPase subunit B in PDB entry 5voz, assembly 1, front view.
V-type proton ATPase subunit B in PDB entry 5voz, assembly 1, side view.
V-type proton ATPase subunit B in PDB entry 5voz, assembly 1, top view.
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V-type proton ATPase subunit E
Chains: G, I, K
Length: 233 amino acids
Theoretical weight: 26.51 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P22203 (Residues: 1-233; Coverage: 100%)
Gene names: O6241, VAT5, VMA4, YOR332W
Pfam: ATP synthase (E/31 kDa) subunit
InterPro:
V-type proton ATPase subunit E in PDB entry 5voz, assembly 1, front view.
V-type proton ATPase subunit E in PDB entry 5voz, assembly 1, side view.
V-type proton ATPase subunit E in PDB entry 5voz, assembly 1, top view.
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V-type proton ATPase subunit G
Chains: H, J, L
Length: 114 amino acids
Theoretical weight: 12.74 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P48836 (Residues: 1-114; Coverage: 100%)
Gene names: VMA10, YHR039BC, YHR039C-A, YHR039C-B
Pfam: Vacuolar (H+)-ATPase G subunit
InterPro: Vacuolar (H+)-ATPase G subunit
V-type proton ATPase subunit G in PDB entry 5voz, assembly 1, front view.
V-type proton ATPase subunit G in PDB entry 5voz, assembly 1, side view.
V-type proton ATPase subunit G in PDB entry 5voz, assembly 1, top view.
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V-type proton ATPase subunit D
Chain: M
Length: 256 amino acids
Theoretical weight: 29.24 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32610 (Residues: 1-256; Coverage: 100%)
Gene names: SYGP-ORF11, VMA8, YEL051W
Pfam: ATP synthase subunit D
InterPro: ATPase, V1 complex, subunit D
V-type proton ATPase subunit D in PDB entry 5voz, assembly 1, front view.
V-type proton ATPase subunit D in PDB entry 5voz, assembly 1, side view.
V-type proton ATPase subunit D in PDB entry 5voz, assembly 1, top view.
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V-type proton ATPase subunit F
Chain: N
Length: 118 amino acids
Theoretical weight: 13.48 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P39111 (Residues: 1-118; Coverage: 100%)
Gene names: VMA7, YGR020C
Pfam: ATP synthase (F/14-kDa) subunit
InterPro:
V-type proton ATPase subunit F in PDB entry 5voz, assembly 1, front view.
V-type proton ATPase subunit F in PDB entry 5voz, assembly 1, side view.
V-type proton ATPase subunit F in PDB entry 5voz, assembly 1, top view.
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V-type proton ATPase subunit C
Chain: O
Length: 392 amino acids
Theoretical weight: 44.24 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P31412 (Residues: 1-392; Coverage: 100%)
Gene names: VAT3, VATC, VMA5, YKL080W, YKL410
Pfam: V-ATPase subunit C
InterPro:
V-type proton ATPase subunit C in PDB entry 5voz, assembly 1, front view.
V-type proton ATPase subunit C in PDB entry 5voz, assembly 1, side view.
V-type proton ATPase subunit C in PDB entry 5voz, assembly 1, top view.
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V-type proton ATPase subunit H
Chain: P
Length: 478 amino acids
Theoretical weight: 54.48 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P41807 (Residues: 1-478; Coverage: 100%)
Gene names: CLS11, VMA13, YP3085.02, YPR036W
Pfam:
InterPro:
V-type proton ATPase subunit H in PDB entry 5voz, assembly 1, front view.
V-type proton ATPase subunit H in PDB entry 5voz, assembly 1, side view.
V-type proton ATPase subunit H in PDB entry 5voz, assembly 1, top view.
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V-type proton ATPase subunit d
Chain: Q
Length: 345 amino acids
Theoretical weight: 39.82 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32366 (Residues: 1-345; Coverage: 100%)
Gene names: L9324.8, VMA6, YLR447C
Pfam: ATP synthase (C/AC39) subunit
InterPro:
V-type proton ATPase subunit d in PDB entry 5voz, assembly 1, front view.
V-type proton ATPase subunit d in PDB entry 5voz, assembly 1, side view.
V-type proton ATPase subunit d in PDB entry 5voz, assembly 1, top view.
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V-type proton ATPase subunit c''
Chain: R
Length: 213 amino acids
Theoretical weight: 22.61 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P23968 (Residues: 1-213; Coverage: 100%)
Gene names: PPA1, VMA16, YHR026W
Pfam: ATP synthase subunit C
InterPro:
V-type proton ATPase subunit c'' in PDB entry 5voz, assembly 1, front view.
V-type proton ATPase subunit c'' in PDB entry 5voz, assembly 1, side view.
V-type proton ATPase subunit c'' in PDB entry 5voz, assembly 1, top view.
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V-type proton ATPase subunit c'
Chain: S
Length: 164 amino acids
Theoretical weight: 17.05 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32842 (Residues: 1-164; Coverage: 100%)
Gene names: CLS9, P1064, TFP3, VMA11, YPL234C
Pfam: ATP synthase subunit C
InterPro:
V-type proton ATPase subunit c' in PDB entry 5voz, assembly 1, front view.
V-type proton ATPase subunit c' in PDB entry 5voz, assembly 1, side view.
V-type proton ATPase subunit c' in PDB entry 5voz, assembly 1, top view.
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V-type proton ATPase subunit c
Chains: T, U, V, W, X, Y, Z, a
Length: 160 amino acids
Theoretical weight: 16.36 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P25515 (Residues: 1-160; Coverage: 100%)
Gene names: CLS7, CUP5, GEF2, VMA3, YEL027W
Pfam: ATP synthase subunit C
InterPro:
V-type proton ATPase subunit c in PDB entry 5voz, assembly 1, front view.
V-type proton ATPase subunit c in PDB entry 5voz, assembly 1, side view.
V-type proton ATPase subunit c in PDB entry 5voz, assembly 1, top view.
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V-type proton ATPase subunit a, vacuolar isoform
Chain: b
Length: 840 amino acids
Theoretical weight: 95.63 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32563 (Residues: 1-840; Coverage: 100%)
Gene names: VPH1, YOR270C
Pfam: V-type ATPase 116kDa subunit family
InterPro:
V-type proton ATPase subunit a, vacuolar isoform in PDB entry 5voz, assembly 1, front view.
V-type proton ATPase subunit a, vacuolar isoform in PDB entry 5voz, assembly 1, side view.
V-type proton ATPase subunit a, vacuolar isoform in PDB entry 5voz, assembly 1, top view.
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V-type proton ATPase subunit e
Chain: c
Length: 73 amino acids
Theoretical weight: 8.39 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q3E7B6 (Residues: 1-73; Coverage: 100%)
Gene names: CWH36, LDB10, VMA9, YCL005W-A
Pfam: ATP synthase subunit H
InterPro: ATPase, V0 complex, subunit e1/e2
V-type proton ATPase subunit e in PDB entry 5voz, assembly 1, front view.
V-type proton ATPase subunit e in PDB entry 5voz, assembly 1, side view.
V-type proton ATPase subunit e in PDB entry 5voz, assembly 1, top view.
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V-type proton ATPase subunit f
Chain: d
Length: 54 amino acids
Theoretical weight: 4.61 KDa
Source organism: Saccharomyces cerevisiae S288C
V-type proton ATPase subunit f in PDB entry 5voz, assembly 1, front view.
V-type proton ATPase subunit f in PDB entry 5voz, assembly 1, side view.
V-type proton ATPase subunit f in PDB entry 5voz, assembly 1, top view.
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Uncharacterized protein
Chains: e, f, g
Length: 573 amino acids
Theoretical weight: 65.49 KDa
Source organism: Legionella pneumophila subsp. pneumophila ATCC 43290
Expression system: Escherichia coli
Uncharacterized protein in PDB entry 5voz, assembly 1, front view.
Uncharacterized protein in PDB entry 5voz, assembly 1, side view.
Uncharacterized protein in PDB entry 5voz, assembly 1, top view.
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