5VOX

Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 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
  • Primary Citation of Related Structures:  

  • 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

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase catalytic subunit A,V-type proton ATPase catalytic subunit A
A, C, E
617Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA1 (CLS8, TFP1)
EC: 3.6.3.14
Find proteins for P17255 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P17255
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit B
B, D, F
517Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA2 (VAT2)
Find proteins for P16140 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P16140
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit E
G, I, K
233Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA4 (VAT5)
Find proteins for P22203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22203
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit G
H, J, L
114Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA10
Find proteins for P48836 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P48836
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit D
M
256Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA8
Find proteins for P32610 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32610
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit F
N
118Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA7
Find proteins for P39111 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39111
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit C
O
392Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA5 (VAT3, VATC)
Find proteins for P31412 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P31412
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit H
P
478Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA13 (CLS11)
Find proteins for P41807 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P41807
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit d
Q
345Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA6
Find proteins for P32366 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32366
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit c''
R
213Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA16 (PPA1)
Find proteins for P23968 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23968
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit c'
S
164Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA11 (CLS9, TFP3)
Find proteins for P32842 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32842
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit c
T, U, V, W, X, Y, Z, a
160Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA3 (CLS7, CUP5, GEF2)
Find proteins for P25515 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25515
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit a, vacuolar isoform
b
840Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VPH1
Find proteins for P32563 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32563
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit e
c
73Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA9 (CWH36, LDB10)
Find proteins for Q3E7B6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q3E7B6
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit f
d
54N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
effector protein SidK
e, f, g
573N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
d
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-05-03 
  • Released Date: 2017-06-21 
  • Deposition Author(s): Zhao, J.

Funding OrganizationLocationGrant Number
Canadian Institutes of Health ResearchCanadaMOP 81294
Canadian Institutes of Health ResearchCanadaMOP-48370
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR56AI103168
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR21AI10571
Natural Sciences and Engineering Research Council (Canada)CanadaRGPIN-2015-05372

Revision History 

  • Version 1.0: 2017-06-21
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence, Data collection