3J9V

Yeast V-ATPase state 3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.3 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:  

  • 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit a, vacuolar isoform
b
840Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VPH1
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Heterotrimeric EGChead Peripheral Stalk Complex
Find proteins for P32563 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32563
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit C
O
392Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA5 (VAT3, VATC)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Heterotrimeric EGChead Peripheral Stalk Complex
Find proteins for P31412 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P31412
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit D
M
256Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA8
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Heterotrimeric EGChead Peripheral Stalk Complex
Find proteins for P32610 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32610
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit F
N
118Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA7
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Heterotrimeric EGChead Peripheral Stalk Complex
Find proteins for P39111 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39111
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase catalytic subunit A
E, A, C
616Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA1 (CLS8, TFP1)
EC: 7.1.2.2
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Heterotrimeric EGChead Peripheral Stalk Complex
Find proteins for P17255 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P17255
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit B
F, B, D
517Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA2 (VAT2)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Heterotrimeric EGChead Peripheral Stalk Complex
Find proteins for P16140 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P16140
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit d
Q
345Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA6
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Heterotrimeric EGChead Peripheral Stalk Complex
Find proteins for P32366 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32366
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit G
J, L, H
114Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA10
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Heterotrimeric EGChead Peripheral Stalk Complex
Find proteins for P48836 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P48836
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit E
I, K, G
233Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA4 (VAT5)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Heterotrimeric EGChead Peripheral Stalk Complex
Find proteins for P22203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22203
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit H
P
478Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA13 (CLS11)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Heterotrimeric EGChead Peripheral Stalk Complex
Find proteins for P41807 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P41807
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit c
R, U, X, Y, W, Z, V, a, S, T
160Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA3 (CLS7, CUP5, GEF2)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Heterotrimeric EGChead Peripheral Stalk Complex
Find proteins for P25515 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25515
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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