6PE4 image
Entry Detail
PDB ID:
6PE4
EMDB ID:
Title:
Yeast Vo motor in complex with 1 VopQ molecule
Biological Source:
PDB Version:
Deposition Date:
2019-06-20
Release Date:
2020-05-20
Method Details:
Experimental Method:
Resolution:
3.10 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:V-type proton ATPase subunit a, vacuolar isoform
Chain IDs:A
Chain Length:1012
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:V0 assembly protein 1
Chain IDs:B
Chain Length:265
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:V-type proton ATPase subunit d
Chain IDs:C (auth: D)
Chain Length:345
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:V-type proton ATPase subunit e
Chain IDs:D (auth: E)
Chain Length:73
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:Uncharacterized protein YPR170W-B
Chain IDs:E (auth: F)
Chain Length:85
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:V-type proton ATPase subunit c''
Chain IDs:F (auth: G)
Chain Length:213
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:V-type proton ATPase subunit c'
Chain IDs:G (auth: H)
Chain Length:164
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:V-type proton ATPase subunit c
Chain IDs:H (auth: I), I (auth: J), J (auth: K), K (auth: L), L (auth: M), M (auth: N), N (auth: O), O (auth: P)
Chain Length:160
Number of Molecules:8
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:Cation transporter
Chain IDs:P (auth: Q)
Chain Length:513
Number of Molecules:1
Biological Source:Vibrio parahaemolyticus
Ligand Molecules
Primary Citation
A distinct inhibitory mechanism of the V-ATPase by Vibrio VopQ revealed by cryo-EM.
Nat.Struct.Mol.Biol. 27 589 597 (2020)
PMID: 32424347 DOI: 10.1038/s41594-020-0429-1

Abstact

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 Vo 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 Vo. We show that VopQ arrests yeast growth in vivo by targeting the immature Vo 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.

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Primary Citation of related structures