5VOZ

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Molecular basis for the binding and modulation of V-ATPase by a bacterial effector protein.

Zhao, J.Beyrakhova, K.Liu, Y.Alvarez, C.P.Bueler, S.A.Xu, L.Xu, C.Boniecki, M.T.Kanelis, V.Luo, Z.Q.Cygler, M.Rubinstein, J.L.

(2017) PLoS Pathog 13: e1006394-e1006394

  • DOI: https://doi.org/10.1371/journal.ppat.1006394
  • Primary Citation of Related Structures:  
    5UF5, 5UFK, 5VOX, 5VOY, 5VOZ

  • PubMed Abstract: 

    Intracellular pathogenic bacteria evade the immune response by replicating within host cells. Legionella pneumophila, the causative agent of Legionnaires' Disease, makes use of numerous effector proteins to construct a niche supportive of its replication within phagocytic cells. The L. pneumophila effector SidK was identified in a screen for proteins that reduce the activity of the proton pumping vacuolar-type ATPases (V-ATPases) when expressed in the yeast Saccharomyces cerevisae. SidK is secreted by L. pneumophila in the early stages of infection and by binding to and inhibiting the V-ATPase, SidK reduces phagosomal acidification and promotes survival of the bacterium inside macrophages. We determined crystal structures of the N-terminal region of SidK at 2.3 Å resolution and used single particle electron cryomicroscopy (cryo-EM) to determine structures of V-ATPase:SidK complexes at ~6.8 Å resolution. SidK is a flexible and elongated protein composed of an α-helical region that interacts with subunit A of the V-ATPase and a second region of unknown function that is flexibly-tethered to the first. SidK binds V-ATPase strongly by interacting via two α-helical bundles at its N terminus with subunit A. In vitro activity assays show that SidK does not inhibit the V-ATPase completely, but reduces its activity by ~40%, consistent with the partial V-ATPase deficiency phenotype its expression causes in yeast. The cryo-EM analysis shows that SidK reduces the flexibility of the A-subunit that is in the 'open' conformation. Fluorescence experiments indicate that SidK binding decreases the affinity of V-ATPase for a fluorescent analogue of ATP. Together, these results reveal the structural basis for the fine-tuning of V-ATPase activity by SidK.


  • Organizational Affiliation

    The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase catalytic subunit A,V-type proton ATPase catalytic subunit A
A, C, E
617Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.6.3.14 (PDB Primary Data), 3.1 (PDB Primary Data), 7.1.2.2 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P17255 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit B
B, D, F
517Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P16140 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit E
G, I, K
233Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit G
H, J, L
114Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit D256Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit F118Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit C392Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit H478Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit d345Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit c''213Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit c'164Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit c
AA [auth a],
T,
U,
V,
W,
X,
Y,
Z
160Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit a, vacuolar isoformBA [auth b]840Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit eCA [auth c]73Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit fDA [auth d]54Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinEA [auth e],
FA [auth f],
GA [auth g]
573Legionella pneumophila subsp. pneumophila ATCC 43290Mutation(s): 0 
Gene Names: lp12_0990
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2017-06-28 
  • Deposition Author(s): Zhao, J.

Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaMOP 81294
Canadian Institutes of Health Research (CIHR)CanadaMOP-48370
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR56AI103168
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21AI10571
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaRGPIN-2015-05372

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-05
    Changes: Database references
  • Version 1.2: 2017-07-26
    Changes: Author supporting evidence, Data collection, Database references
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references