3J9V

Yeast V-ATPase state 3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Electron cryomicroscopy observation of rotational states in a eukaryotic V-ATPase.

Zhao, J.Benlekbir, S.Rubinstein, J.L.

(2015) Nature 521: 241-245

  • DOI: 10.1038/nature14365
  • Primary Citation of Related Structures:  
    3J9T, 3J9U, 3J9V

  • PubMed Abstract: 
  • Eukaryotic vacuolar H(+)-ATPases (V-ATPases) are rotary enzymes that use energy from hydrolysis of ATP to ADP to pump protons across membranes and control the pH of many intracellular compartments. ATP hydrolysis in the soluble catalytic region of th ...

    Eukaryotic vacuolar H(+)-ATPases (V-ATPases) are rotary enzymes that use energy from hydrolysis of ATP to ADP to pump protons across membranes and control the pH of many intracellular compartments. ATP hydrolysis in the soluble catalytic region of the enzyme is coupled to proton translocation through the membrane-bound region by rotation of a central rotor subcomplex, with peripheral stalks preventing the entire membrane-bound region from turning with the rotor. The eukaryotic V-ATPase is the most complex rotary ATPase: it has three peripheral stalks, a hetero-oligomeric proton-conducting proteolipid ring, several subunits not found in other rotary ATPases, and is regulated by reversible dissociation of its catalytic and proton-conducting regions. Studies of ATP synthases, V-ATPases, and bacterial/archaeal V/A-ATPases have suggested that flexibility is necessary for the catalytic mechanism of rotary ATPases, but the structures of different rotational states have never been observed experimentally. Here we use electron cryomicroscopy to obtain structures for three rotational states of the V-ATPase from the yeast Saccharomyces cerevisiae. The resulting series of structures shows ten proteolipid subunits in the c-ring, setting the ATP:H(+) ratio for proton pumping by the V-ATPase at 3:10, and reveals long and highly tilted transmembrane α-helices in the a-subunit that interact with the c-ring. The three different maps reveal the conformational changes that occur to couple rotation in the symmetry-mismatched soluble catalytic region to the membrane-bound proton-translocating region. Almost all of the subunits of the enzyme undergo conformational changes during the transitions between these three rotational states. The structures of these states provide direct evidence that deformation during rotation enables the smooth transmission of power through rotary ATPases.


    Organizational Affiliation

    1] Molecular Structure and Function Program, The Hospital for Sick Children Research Institute, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada [2] Department of Medical Biophysics, The University of Toronto, Toronto Medical Discovery Tower, MaRS Centre, 101 College Street, Toronto, Ontario M5G 1L7, Canada [3] Department of Biochemistry, The University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, Ontario M5S 1A8, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit a, vacuolar isoformb840Saccharomyces cerevisiaeMutation(s): 0 
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Complete V-ATPase by cryo-EM, state 1
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
V-type proton ATPase subunit CO392Saccharomyces cerevisiaeMutation(s): 0 
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Complete V-ATPase by cryo-EM, state 1
Find proteins for P31412 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P31412 
Go to UniProtKB:  P31412
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit DM256Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P32610 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32610 
Go to UniProtKB:  P32610
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit FN118Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P39111 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39111 
Go to UniProtKB:  P39111
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase catalytic subunit AACE616Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.3.14 (PDB Primary Data), 3.1 (PDB Primary Data), 7.1.2.2 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Complete V-ATPase by cryo-EM, state 1
Find proteins for P17255 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P17255 
Go to UniProtKB:  P17255
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit BBDF517Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P16140 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P16140 
Go to UniProtKB:  P16140
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit dQ345Saccharomyces cerevisiaeMutation(s): 0 
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Complete V-ATPase by cryo-EM, state 1
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: 8
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit GHJL114Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P48836 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P48836 
Go to UniProtKB:  P48836
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit EGIK233Saccharomyces cerevisiaeMutation(s): 0 
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Complete V-ATPase by cryo-EM, state 1
Find proteins for P22203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P22203 
Go to UniProtKB:  P22203
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit HP478Saccharomyces cerevisiaeMutation(s): 0 
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Complete V-ATPase by cryo-EM, state 1
Find proteins for P41807 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P41807 
Go to UniProtKB:  P41807
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit cRSTUVWXYZa160Saccharomyces cerevisiaeMutation(s): 0 
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Complete V-ATPase by cryo-EM, state 1
Find proteins for P25515 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25515 
Go to UniProtKB:  P25515
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-13
    Type: Initial release
  • Version 1.1: 2015-05-20
    Changes: Database references
  • Version 1.2: 2015-06-03
    Changes: Database references
  • Version 1.3: 2018-07-18
    Changes: Data collection