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- PDB-7tmm: Complete V1 Complex from Saccharomyces cerevisiae -

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Basic information

Entry
Database: PDB / ID: 7tmm
TitleComplete V1 Complex from Saccharomyces cerevisiae
Components
  • (V-type proton ATPase subunit ...) x 5
  • H(+)-transporting two-sector ATPase
  • V-ATPase subunit E
  • Vacuolar proton pump subunit B
KeywordsHYDROLASE / V-ATPase
Function / homology
Function and homology information


proton-transporting V-type ATPase, V1 domain / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / proton-transporting two-sector ATPase complex, catalytic domain / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar proton-transporting V-type ATPase complex ...proton-transporting V-type ATPase, V1 domain / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / proton-transporting two-sector ATPase complex, catalytic domain / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar proton-transporting V-type ATPase complex / proton-transporting V-type ATPase complex / vacuolar acidification / fungal-type vacuole membrane / ATP metabolic process / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / Golgi membrane / ATP binding
Similarity search - Function
ATPase, V1 complex, subunit H / ATPase, V1 complex, subunit H, C-terminal / ATPase, V1 complex, subunit H, C-terminal domain superfamily / V-ATPase subunit H / V-ATPase subunit H / ATPase, V1 complex, subunit C / Vacuolar ATP synthase subunit C superfamily / V-ATPase subunit C / ATPase, V1 complex, subunit B / ATPase, V1 complex, subunit F, eukaryotic ...ATPase, V1 complex, subunit H / ATPase, V1 complex, subunit H, C-terminal / ATPase, V1 complex, subunit H, C-terminal domain superfamily / V-ATPase subunit H / V-ATPase subunit H / ATPase, V1 complex, subunit C / Vacuolar ATP synthase subunit C superfamily / V-ATPase subunit C / ATPase, V1 complex, subunit B / ATPase, V1 complex, subunit F, eukaryotic / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase (E/31 kDa) subunit / ATPase, V1 complex, subunit D / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / ATP synthase subunit D / ATP synthase (F/14-kDa) subunit / V-type ATP synthase regulatory subunit B/beta / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Armadillo-like helical / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / V-type proton ATPase subunit C / V-type proton ATPase subunit F / VMA8 isoform 1 / Vacuolar proton pump subunit B / VMA4 isoform 1 / : / : / V-type proton ATPase subunit H
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsVasanthakumar, T. / Keon, K.A. / Bueler, S.A. / Jaskolka, M.C. / Rubinstein, J.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT166152 Canada
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: Coordinated conformational changes in the V complex during V-ATPase reversible dissociation.
Authors: Thamiya Vasanthakumar / Kristine A Keon / Stephanie A Bueler / Michael C Jaskolka / John L Rubinstein /
Abstract: Vacuolar-type ATPases (V-ATPases) are rotary enzymes that acidify intracellular compartments in eukaryotic cells. These multi-subunit complexes consist of a cytoplasmic V region that hydrolyzes ATP ...Vacuolar-type ATPases (V-ATPases) are rotary enzymes that acidify intracellular compartments in eukaryotic cells. These multi-subunit complexes consist of a cytoplasmic V region that hydrolyzes ATP and a membrane-embedded V region that transports protons. V-ATPase activity is regulated by reversible dissociation of the two regions, with the isolated V and V complexes becoming autoinhibited on disassembly and subunit C subsequently detaching from V. In yeast, assembly of the V and V regions is mediated by the regulator of the ATPase of vacuoles and endosomes (RAVE) complex through an unknown mechanism. We used cryogenic-electron microscopy of yeast V-ATPase to determine structures of the intact enzyme, the dissociated but complete V complex and the V complex lacking subunit C. On separation, V undergoes a dramatic conformational rearrangement, with its rotational state becoming incompatible for reassembly with V. Loss of subunit C allows V to match the rotational state of V, suggesting how RAVE could reassemble V and V by recruiting subunit C.
History
DepositionJan 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jun 1, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H(+)-transporting two-sector ATPase
B: Vacuolar proton pump subunit B
C: H(+)-transporting two-sector ATPase
D: Vacuolar proton pump subunit B
E: H(+)-transporting two-sector ATPase
F: Vacuolar proton pump subunit B
G: V-ATPase subunit E
H: V-type proton ATPase subunit G
I: V-ATPase subunit E
J: V-type proton ATPase subunit G
K: V-ATPase subunit E
L: V-type proton ATPase subunit G
M: V-type proton ATPase subunit D
N: V-type proton ATPase subunit F
O: V-type proton ATPase subunit C
P: V-type proton ATPase subunit H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)644,59717
Polymers644,17016
Non-polymers4271
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 9 molecules ACEBDFGIK

#1: Protein H(+)-transporting two-sector ATPase


Mass: 70515.203 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: A0A6L0YX77, H+-transporting two-sector ATPase
#2: Protein Vacuolar proton pump subunit B / V-ATPase subunit B / Vacuolar proton pump subunit B


Mass: 57815.023 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q585
#3: Protein V-ATPase subunit E / HLJ1_G0040890.mRNA.1.CDS.1


Mass: 26508.393 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q7Y8

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V-type proton ATPase subunit ... , 5 types, 7 molecules HJLMNOP

#4: Protein V-type proton ATPase subunit G


Mass: 12738.706 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6L0ZI53
#5: Protein V-type proton ATPase subunit D / HLJ1_G0000250.mRNA.1.CDS.1 / HN1_G0000230.mRNA.1.CDS.1 / SX2_G0000250.mRNA.1.CDS.1 / Y55_G0000250.mRNA.1.CDS.1


Mass: 29235.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q1W2
#6: Protein V-type proton ATPase subunit F


Mass: 13479.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PYF6
#7: Protein V-type proton ATPase subunit C


Mass: 44241.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PTP1
#8: Protein V-type proton ATPase subunit H / V-ATPase subunit H / V-ATPase 54 kDa subunit / Vacuolar proton pump subunit H


Mass: 54482.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41807

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Non-polymers , 1 types, 1 molecules

#9: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestY

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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

ComponentName: Complete V1 Complex / Type: COMPLEX
Details: Complete V1 complex from yeast V-ATPase following dissociation
Entity ID: #1-#8 / Source: NATURAL
Molecular weightValue: 0.635 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 43 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 105017 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00534295
ELECTRON MICROSCOPYf_angle_d0.52647168
ELECTRON MICROSCOPYf_dihedral_angle_d4.4955551
ELECTRON MICROSCOPYf_chiral_restr0.0425919
ELECTRON MICROSCOPYf_plane_restr0.0046192

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