6C6L

Yeast Vacuolar ATPase Vo in lipid nanodisc


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

The 3.5- angstrom CryoEM Structure of Nanodisc-Reconstituted Yeast Vacuolar ATPase VoProton Channel.

Roh, S.H.Stam, N.J.Hryc, C.F.Couoh-Cardel, S.Pintilie, G.Chiu, W.Wilkens, S.

(2018) Mol Cell 69: 993-1004.e3

  • DOI: https://doi.org/10.1016/j.molcel.2018.02.006
  • Primary Citation of Related Structures:  
    6C6L

  • PubMed Abstract: 

    The molecular mechanism of transmembrane proton translocation in rotary motor ATPases is not fully understood. Here, we report the 3.5-Å resolution cryoEM structure of the lipid nanodisc-reconstituted V o proton channel of the yeast vacuolar H + -ATPase, captured in a physiologically relevant, autoinhibited state. The resulting atomic model provides structural detail for the amino acids that constitute the proton pathway at the interface of the proteolipid ring and subunit a. Based on the structure and previous mutagenesis studies, we propose the chemical basis of transmembrane proton transport. Moreover, we discovered that the C terminus of the assembly factor Voa1 is an integral component of mature V o . Voa1's C-terminal transmembrane α helix is bound inside the proteolipid ring, where it contributes to the stability of the complex. Our structure rationalizes possible mechanisms by which mutations in human V o can result in disease phenotypes and may thus provide new avenues for therapeutic interventions.


  • Organizational Affiliation

    Department of Bioengineering and James H. Clark Center, Stanford University, Stanford, CA 94305, USA; Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit c'A [auth D]164Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P32842 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P32842
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UniProt GroupP32842
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit c''B [auth C]213Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P23968 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP23968
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
V0 assembly protein 1C [auth N]265Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P53262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP53262
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit eD [auth M]73Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q3E7B6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupQ3E7B6
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit c160Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.6.3.14
Membrane Entity: Yes 
UniProt
Find proteins for P25515 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP25515
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit dF [auth B]345Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P32366 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit a, vacuolar isoformN [auth A]840Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P32563 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP32563
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit f85Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0C5R9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4

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 StatesGM058600
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103832
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM079429
National Institutes of Health/National Library of Medicine (NIH/NLM)United StatesT15LM007093

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2018-03-28
    Changes: Data collection, Database references
  • Version 1.2: 2018-07-18
    Changes: Data collection, Experimental preparation
  • Version 1.3: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2019-12-18
    Changes: Author supporting evidence, Other
  • Version 1.5: 2024-03-13
    Changes: Data collection, Database references