6PE4

Yeast Vo motor in complex with 1 VopQ molecule


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A distinct inhibitory mechanism of the V-ATPase by Vibrio VopQ revealed by cryo-EM.

Peng, W.Casey, A.K.Fernandez, J.Carpinone, E.M.Servage, K.A.Chen, Z.Li, Y.Tomchick, D.R.Starai, V.J.Orth, K.

(2020) Nat Struct Mol Biol 27: 589-597

  • DOI: 10.1038/s41594-020-0429-1
  • Primary Citation of Related Structures:  
    6PE4, 6PE5

  • PubMed Abstract: 
  • The Vibrio parahaemolyticus T3SS effector VopQ targets host-cell V-ATPase, resulting in blockage of autophagic flux and neutralization of acidic compartments. Here, we report the cryo-EM structure of VopQ bound to the V o subcomplex of th ...

    The Vibrio parahaemolyticus T3SS effector VopQ targets host-cell V-ATPase, resulting in blockage of autophagic flux and neutralization of acidic compartments. Here, we report the cryo-EM structure of VopQ bound to the V o subcomplex of the V-ATPase. VopQ inserts into membranes and forms an unconventional pore while binding directly to subunit c of the V-ATPase membrane-embedded subcomplex V o . We show that VopQ arrests yeast growth in vivo by targeting the immature V o subcomplex in the endoplasmic reticulum (ER), thus providing insight into the observation that VopQ kills cells in the absence of a functional V-ATPase. VopQ is a bacterial effector that has been discovered to inhibit a host-membrane megadalton complex by coincidentally binding its target, inserting into a membrane and disrupting membrane potential. Collectively, our results reveal a mechanism by which bacterial effectors modulate host cell biology and provide an invaluable tool for future studies on V-ATPase-mediated membrane fusion and autophagy.


    Organizational Affiliation

    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA. Kim.Orth@UTSouthwestern.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit a, vacuolar isoformA1012Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VPH1YOR270C
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
VO motor of V-ATPase in complex with 1 VopQ toxin
Find proteins for P32563 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32563 
Go to UniProtKB:  P32563
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
V0 assembly protein 1B265Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VOA1YGR106C
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
VO motor of V-ATPase in complex with 1 VopQ toxin
Find proteins for P53262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53262 
Go to UniProtKB:  P53262
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit dD345Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA6YLR447CL9324.8
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
VO motor of V-ATPase in complex with 1 VopQ toxin
Find proteins for P32366 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32366 
Go to UniProtKB:  P32366
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit eE73Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA9CWH36LDB10YCL005W-A
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
VO motor of V-ATPase in complex with 1 VopQ toxin
Find proteins for Q3E7B6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q3E7B6 
Go to UniProtKB:  Q3E7B6
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein YPR170W-BF85Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YPR170W-B
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
VO motor of V-ATPase in complex with 1 VopQ toxin
Find proteins for P0C5R9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0C5R9 
Go to UniProtKB:  P0C5R9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit c''G213Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA16PPA1YHR026W
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
VO motor of V-ATPase in complex with 1 VopQ toxin
Find proteins for P23968 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P23968 
Go to UniProtKB:  P23968
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit c'H164Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA11CLS9TFP3YPL234CP1064
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
VO motor of V-ATPase in complex with 1 VopQ toxin
Find proteins for P32842 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32842 
Go to UniProtKB:  P32842
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit cIJKLMNOP160Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA3CLS7CUP5GEF2YEL027W
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
VO motor of V-ATPase in complex with 1 VopQ toxin
Find proteins for P25515 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25515 
Go to UniProtKB:  P25515
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Cation transporterQ513Vibrio parahaemolyticusMutation(s): 0 
Gene Names: ACS91_23375CGH73_02470
Find proteins for A0A4Z7TVW3 (Vibrio parahaemolyticus)
Explore A0A4Z7TVW3 
Go to UniProtKB:  A0A4Z7TVW3
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--
Welch FoundationUnited States--

Revision History 

  • Version 1.0: 2020-05-20
    Type: Initial release
  • Version 1.1: 2020-06-03
    Changes: Database references
  • Version 1.2: 2020-06-24
    Changes: Database references