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- PDB-8eas: Yeast VO in complex with Vma12-22p -

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Basic information

Entry
Database: PDB / ID: 8eas
TitleYeast VO in complex with Vma12-22p
Components
  • (V-type proton ATPase subunit ...) x 7
  • V-type proton ATPase assembly factor Vma12p
  • V0 assembly protein 1
  • Vacuolar ATPase assembly protein VMA22
  • Yeast V-ATPase subunit f
KeywordsMEMBRANE PROTEIN / V-type / ATPase / assembly / proton
Function / homology
Function and homology information


Vma12-Vma22 assembly complex / vacuolar proton-transporting V-type ATPase complex assembly / cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / cellular response to alkaline pH / protein localization to vacuolar membrane / proton-transporting V-type ATPase, V1 domain / Insulin receptor recycling / Transferrin endocytosis and recycling / polyphosphate metabolic process ...Vma12-Vma22 assembly complex / vacuolar proton-transporting V-type ATPase complex assembly / cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / cellular response to alkaline pH / protein localization to vacuolar membrane / proton-transporting V-type ATPase, V1 domain / Insulin receptor recycling / Transferrin endocytosis and recycling / polyphosphate metabolic process / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / P-type proton-exporting transporter activity / vacuolar transport / vacuolar proton-transporting V-type ATPase, V0 domain / endosomal lumen acidification / vacuole organization / protein targeting to vacuole / proton-transporting V-type ATPase complex / fungal-type vacuole / vacuolar proton-transporting V-type ATPase complex / cellular hyperosmotic response / vacuolar acidification / fungal-type vacuole membrane / phosphatidylinositol-3,5-bisphosphate binding / proton transmembrane transporter activity / proton-transporting ATPase activity, rotational mechanism / intracellular copper ion homeostasis / Neutrophil degranulation / RNA endonuclease activity / proton transmembrane transport / cell periphery / transmembrane transport / endocytosis / unfolded protein binding / ATPase binding / protein-containing complex assembly / intracellular iron ion homeostasis / membrane raft / Golgi membrane / endoplasmic reticulum membrane / nucleus / membrane
Similarity search - Function
Vma22/CCDC115 / Vma22/CCDC115 / lithium bound rotor ring of v- atpase / Ribonuclease kappa / : / V-type proton ATPase subunit f-like / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / ATPase, V1 complex, subunit F, eukaryotic / ATPase, V0 complex, subunit e1/e2 ...Vma22/CCDC115 / Vma22/CCDC115 / lithium bound rotor ring of v- atpase / Ribonuclease kappa / : / V-type proton ATPase subunit f-like / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / ATPase, V1 complex, subunit F, eukaryotic / ATPase, V0 complex, subunit e1/e2 / ATP synthase subunit H / ATPase, V0 complex, subunit d / V-ATPase proteolipid subunit C, eukaryotic / ATPase, V0 complex, subunit 116kDa, eukaryotic / ATPase, V0 complex, c/d subunit / V-type ATPase subunit C/d / V-type ATP synthase subunit c/d subunit superfamily / V-type ATP synthase c/d subunit, domain 3 superfamily / ATP synthase (C/AC39) subunit / V-ATPase proteolipid subunit / V-type ATPase, V0 complex, 116kDa subunit family / V-type ATPase 116kDa subunit family / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / ATP synthase (F/14-kDa) subunit / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
V-type proton ATPase subunit F / V-type proton ATPase subunit f / V-type proton ATPase subunit c'' / V-type proton ATPase subunit c / V-type proton ATPase subunit d / V-type proton ATPase subunit a, vacuolar isoform / V-type proton ATPase subunit c' / Vacuolar ATPase assembly protein VMA22 / V0 assembly protein 1 / V-type proton ATPase subunit e
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsWang, H. / Bueler, S.A. / Rubinstein, J.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT166152 Canada
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2023
Title: Structural basis of V-ATPase V region assembly by Vma12p, 21p, and 22p.
Authors: Hanlin Wang / Stephanie A Bueler / John L Rubinstein /
Abstract: Vacuolar-type adenosine triphosphatases (V-ATPases) are rotary proton pumps that acidify specific intracellular compartments in almost all eukaryotic cells. These multi-subunit enzymes consist of a ...Vacuolar-type adenosine triphosphatases (V-ATPases) are rotary proton pumps that acidify specific intracellular compartments in almost all eukaryotic cells. These multi-subunit enzymes consist of a soluble catalytic V region and a membrane-embedded proton-translocating V region. V is assembled in the endoplasmic reticulum (ER) membrane, and V is assembled in the cytosol. However, V binds V only after V is transported to the Golgi membrane, thereby preventing acidification of the ER. We isolated V complexes and subcomplexes from bound to V-ATPase assembly factors Vma12p, Vma21p, and Vma22p. Electron cryomicroscopy shows how the Vma12-22p complex recruits subunits a, e, and f to the rotor ring of V while blocking premature binding of V. Vma21p, which contains an ER-retrieval motif, binds the V:Vma12-22p complex, "mature" V, and a complex that appears to contain a ring of loosely packed rotor subunits and the proteins YAR027W and YAR028W. The structures suggest that Vma21p binds assembly intermediates that contain a rotor ring and that activation of proton pumping following assembly of V with V removes Vma21p, allowing V-ATPase to remain in the Golgi. Together, these structures show how Vma12-22p and Vma21p function in V-ATPase assembly and quality control, ensuring the enzyme acidifies only its intended cellular targets.
#1: Journal: Biorxiv / Year: 2022
Title: Structural basis of V-ATPase V0 region assembly by Vma12p, 21p, and 22p
Authors: Wang, H. / Bueler, S.A. / Rubinstein, J.L.
History
DepositionAug 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
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Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3May 21, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vacuolar ATPase assembly protein VMA22
B: V-type proton ATPase assembly factor Vma12p
F: V-type proton ATPase subunit F
a: V-type proton ATPase subunit a, vacuolar isoform
b: V0 assembly protein 1
c: V-type proton ATPase subunit c''
d: V-type proton ATPase subunit d
e: V-type proton ATPase subunit e
f: Yeast V-ATPase subunit f
g: V-type proton ATPase subunit c
h: V-type proton ATPase subunit c
i: V-type proton ATPase subunit c
j: V-type proton ATPase subunit c
k: V-type proton ATPase subunit c
l: V-type proton ATPase subunit c
m: V-type proton ATPase subunit c
n: V-type proton ATPase subunit c
o: V-type proton ATPase subunit c'


Theoretical massNumber of molelcules
Total (without water)404,46118
Polymers404,46118
Non-polymers00
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 , 4 types, 4 molecules ABbf

#1: Protein Vacuolar ATPase assembly protein VMA22


Mass: 21104.717 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38784
#2: Protein V-type proton ATPase assembly factor Vma12p


Mass: 16460.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#5: Protein V0 assembly protein 1


Mass: 29694.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53262
#9: Protein Yeast V-ATPase subunit f


Mass: 9369.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C5R9

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V-type proton ATPase subunit ... , 7 types, 14 molecules Facdeghijklmno

#3: 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
#4: 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: 95625.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32563
#6: Protein V-type proton ATPase subunit c'' / V-ATPase subunit c'' / V-ATPase 22 kDa proteolipid subunit / Vacuolar proton pump c'' subunit


Mass: 22610.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23968
#7: Protein V-type proton ATPase subunit d / V-ATPase subunit d / V-ATPase 39 kDa subunit / V-ATPase subunit M39 / Vacuolar proton pump subunit d


Mass: 39822.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32366
#8: Protein V-type proton ATPase subunit e / V-ATPase subunit e / Low dye-binding protein 10 / Vacuolar proton pump subunit e


Mass: 8387.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q3E7B6
#10: Protein
V-type proton ATPase subunit c / V-ATPase subunit c / Guanine nucleotide exchange factor 2 / V-ATPase 16 kDa proteolipid subunit 1 / ...V-ATPase subunit c / Guanine nucleotide exchange factor 2 / V-ATPase 16 kDa proteolipid subunit 1 / Vacuolar proton pump c subunit


Mass: 16357.501 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25515
#11: Protein V-type proton ATPase subunit c' / V-ATPase subunit c' / Proteolipid protein VMA11 / Trifluoperazine resistance protein 3 / V-ATPase ...V-ATPase subunit c' / Proteolipid protein VMA11 / Trifluoperazine resistance protein 3 / V-ATPase 16 kDa proteolipid subunit 2 / Vacuolar proton pump c' subunit


Mass: 17046.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32842

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Details

Has protein modificationN
Sequence detailsThe full sequence of V-type proton ATPase assembly factor Vma12p is ...The full sequence of V-type proton ATPase assembly factor Vma12p is MFEIKLNDRITEFLRKFKNSAKSNEGIDEDIDLFLKRHAIPMQSLLFYVKEYRKDSDLQC SIKELLKPLEFEFKPKAVRGLHYSEDFKKKLEFLKYQEQELEYQSMVKRSKSVFSLQEDD ELTPSQINKQIKEQVTTVFNVLVSVISVVVAIWYWTGSSTNFPVHVRLLLCLFFGILVLV ADVVVYNSYLKKLEEAKVKEKTKVEKKKVLSKITL

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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: Yeast Vo in complex with Vma12-22p / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid type: Homemade
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN 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: 45 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
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 308537 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00625292
ELECTRON MICROSCOPYf_angle_d0.61734339
ELECTRON MICROSCOPYf_dihedral_angle_d4.4833512
ELECTRON MICROSCOPYf_chiral_restr0.0434076
ELECTRON MICROSCOPYf_plane_restr0.0044296

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