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- PDB-5i1m: Yeast V-ATPase average of densities, a subunit segment -

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Basic information

Entry
Database: PDB / ID: 5i1m
TitleYeast V-ATPase average of densities, a subunit segment
ComponentsV-type proton ATPase subunit a, vacuolar isoform
KeywordsMEMBRANE PROTEIN / V-ATPase / Vo region
Function / homology
Function and homology information


cellular response to alkaline pH / polyphosphate metabolic process / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase complex / fungal-type vacuole / vacuolar acidification ...cellular response to alkaline pH / polyphosphate metabolic process / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase complex / fungal-type vacuole / vacuolar acidification / cellular hyperosmotic response / fungal-type vacuole membrane / phosphatidylinositol-3,5-bisphosphate binding / Neutrophil degranulation / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / ATPase binding / protein-containing complex assembly
Similarity search - Function
ATPase, V0 complex, subunit 116kDa, eukaryotic / V-type ATPase, V0 complex, 116kDa subunit family / V-type ATPase 116kDa subunit family
Similarity search - Domain/homology
V-type proton ATPase subunit a, vacuolar isoform
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7 Å
AuthorsSchep, D.G. / Zhao, J. / Rubinstein, J.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP 81294 Canada
CitationJournal: Proc Natl Acad Sci U S A / Year: 2016
Title: Models for the a subunits of the Thermus thermophilus V/A-ATPase and Saccharomyces cerevisiae V-ATPase enzymes by cryo-EM and evolutionary covariance.
Authors: Daniel G Schep / Jianhua Zhao / John L Rubinstein /
Abstract: Rotary ATPases couple ATP synthesis or hydrolysis to proton translocation across a membrane. However, understanding proton translocation has been hampered by a lack of structural information for the ...Rotary ATPases couple ATP synthesis or hydrolysis to proton translocation across a membrane. However, understanding proton translocation has been hampered by a lack of structural information for the membrane-embedded a subunit. The V/A-ATPase from the eubacterium Thermus thermophilus is similar in structure to the eukaryotic V-ATPase but has a simpler subunit composition and functions in vivo to synthesize ATP rather than pump protons. We determined the T. thermophilus V/A-ATPase structure by cryo-EM at 6.4 Å resolution. Evolutionary covariance analysis allowed tracing of the a subunit sequence within the map, providing a complete model of the rotary ATPase. Comparing the membrane-embedded regions of the T. thermophilus V/A-ATPase and eukaryotic V-ATPase from Saccharomyces cerevisiae allowed identification of the α-helices that belong to the a subunit and revealed the existence of previously unknown subunits in the eukaryotic enzyme. Subsequent evolutionary covariance analysis enabled construction of a model of the a subunit in the S. cerevisae V-ATPase that explains numerous biochemical studies of that enzyme. Comparing the two a subunit structures determined here with a structure of the distantly related a subunit from the bovine F-type ATP synthase revealed a conserved pattern of residues, suggesting a common mechanism for proton transport in all rotary ATPases.
History
DepositionFeb 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Data collection / Other
Category: atom_sites / em_image_scans ...atom_sites / em_image_scans / em_single_particle_entity / pdbx_audit_support
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
V: V-type proton ATPase subunit a, vacuolar isoform


Theoretical massNumber of molelcules
Total (without water)51,5491
Polymers51,5491
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21940 Å2

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Components

#1: Protein V-type proton ATPase subunit a, vacuolar isoform / V-ATPase a 1 subunit / V-ATPase 95 kDa subunit / Vacuolar pH protein 1 / Vacuolar proton pump a ...V-ATPase a 1 subunit / V-ATPase 95 kDa subunit / Vacuolar pH protein 1 / Vacuolar proton pump a subunit / Vacuolar proton translocating ATPase subunit a 1


Mass: 51548.867 Da / Num. of mol.: 1 / Fragment: a subunit (UNP residues 383-840) / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: JTY2 / References: UniProt: P32563

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1V-ATPaseCOMPLEXSix maps of the V-ATPase, averaged with the Vo regions alignedall0NATURAL
2V-ATPase a subunitCOMPLEXSegment of averaged densities from six maps of the V-ATPase, aligned to the a subunit. This does not contain the c ring or micelle, but has some densities that are not assigned to the a subunit and likely represent unknown subunits.all1NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Saccharomyces cerevisiae (brewer's yeast)4932JTY2
32Saccharomyces cerevisiae (brewer's yeast)4932JTY2
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 35.7 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: MDFF / Category: model fitting
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 7 Å / Resolution method: OTHER / Num. of particles: 269377
Details: Resolution is approximated from the resolutions of the aligned and averaged maps that yielded the density.
Symmetry type: POINT

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