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 the V-ATPase ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit a, vacuolar isoformA1012Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VPH1, YOR270C
Membrane Entity: Yes 
UniProt
Find proteins for P32563 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32563 
Go to UniProtKB:  P32563
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32563
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
V0 assembly protein 1B265Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VOA1, YGR106C
Membrane Entity: Yes 
UniProt
Find proteins for P53262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53262 
Go to UniProtKB:  P53262
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53262
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit dC [auth D]345Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA6, YLR447C, L9324.8
Membrane Entity: Yes 
UniProt
Find proteins for P32366 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32366 
Go to UniProtKB:  P32366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32366
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit eD [auth E]73Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA9, CWH36, LDB10, YCL005W-A
Membrane Entity: Yes 
UniProt
Find proteins for Q3E7B6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q3E7B6 
Go to UniProtKB:  Q3E7B6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3E7B6
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein YPR170W-BE [auth F]85Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YPR170W-B
Membrane Entity: Yes 
UniProt
Find proteins for P0C5R9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0C5R9 
Go to UniProtKB:  P0C5R9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C5R9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit c''F [auth G]213Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA16, PPA1, YHR026W
Membrane Entity: Yes 
UniProt
Find proteins for P23968 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P23968 
Go to UniProtKB:  P23968
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23968
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit c'G [auth H]164Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA11, CLS9, TFP3, YPL234C, P1064
Membrane Entity: Yes 
UniProt
Find proteins for P32842 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32842 
Go to UniProtKB:  P32842
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32842
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit c160Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA3, CLS7, CUP5, GEF2, YEL027W
Membrane Entity: Yes 
UniProt
Find proteins for P25515 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25515 
Go to UniProtKB:  P25515
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25515
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Cation transporterP [auth Q]513Vibrio parahaemolyticusMutation(s): 0 
Gene Names: ACS91_23375
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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



View more in-depth experimental data

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  (Full details and data files)

  • 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