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 1.3 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: 10.1371/journal.ppat.1006394
  • Structures With Same Primary Citation

  • 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 replica ...

    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

    Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase catalytic subunit A,V-type proton ATPase catalytic subunit AA, C, E617Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA1
EC: 3.6.3.14 (PDB Primary Data), 3.1 (PDB Primary Data), 7.1.2.2 (UniProt)
Find proteins for P17255 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit BB, D, F517Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA2VAT2YBR127CYBR1002
Find proteins for P16140 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit EG, I, K233Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA4VAT5YOR332WO6241
Find proteins for P22203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit GH, J, L114Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA10YHR039C-AYHR039BCYHR039C-B
Find proteins for P48836 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit DM256Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA8YEL051WSYGP-ORF11
Find proteins for P32610 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit FN118Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA7YGR020C
Find proteins for P39111 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit CO392Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA5VAT3VATCYKL080WYKL410
Find proteins for P31412 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit dQ345Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA6YLR447CL9324.8
Find proteins for P32366 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit c''R213Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA16PPA1YHR026W
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit c'S164Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA11CLS9TFP3YPL234CP1064
Find proteins for P32842 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit cT, U, V, W, X, Y, Z, a160Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA3CLS7CUP5GEF2YEL027W
Find proteins for P25515 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit a, vacuolar isoformb840Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VPH1YOR270C
Find proteins for P32563 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit ec73Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA9CWH36LDB10YCL005W-A
Find proteins for Q3E7B6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit fd54Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized proteine, f, g573Legionella pneumophila subsp. pneumophila ATCC 43290Mutation(s): 0 
Gene Names: lp12_0990
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit HP478Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA13CLS11YPR036WYP3085.02
Find proteins for P41807 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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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

  • Deposited Date: 2017-05-03 
  • 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 

  • 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