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 1.4 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: 10.1016/j.molcel.2018.02.006
  • Structures With Same Primary Citation

  • 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 vacuo ...

    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 Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA. Electronic address: wilkenss@upstate.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit c'D164Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA11CLS9TFP3YPL234CP1064
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
ATPase Vo proton channel reconstituted in nano-discs
Find proteins for P32842 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32842 
Go to UniProtKB:  P32842
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit c''C213Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA16PPA1YHR026W
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
ATPase Vo proton channel reconstituted in nano-discs
Find proteins for P23968 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P23968 
Go to UniProtKB:  P23968
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
V0 assembly protein 1N265Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VOA1YGR106C
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
ATPase Vo proton channel reconstituted in nano-discs
Find proteins for P53262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53262 
Go to UniProtKB:  P53262
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit eM73Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA9CWH36LDB10YCL005W-A
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
ATPase Vo proton channel reconstituted in nano-discs
Find proteins for Q3E7B6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q3E7B6 
Go to UniProtKB:  Q3E7B6
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit cE, F, G, H, I, J, K, L160Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA3CLS7CUP5GEF2YEL027W
EC: 3.6.3.14
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
ATPase Vo proton channel reconstituted in nano-discs
Find proteins for P25515 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25515 
Go to UniProtKB:  P25515
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit dB345Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA6YLR447CL9324.8
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
ATPase Vo proton channel reconstituted in nano-discs
Find proteins for P32366 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32366 
Go to UniProtKB:  P32366
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit a, vacuolar isoformA840Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VPH1YOR270C
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
ATPase Vo proton channel reconstituted in nano-discs
Find proteins for P32563 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32563 
Go to UniProtKB:  P32563
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit fO85Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YPR170W-B
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
ATPase Vo proton channel reconstituted in nano-discs
Find proteins for P0C5R9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0C5R9 
Go to UniProtKB:  P0C5R9
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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 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 

  • 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