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- PDB-8eav: YAR027W and YAR028W in complex with c subunits from yeast VO complex -

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Basic information

Entry
Database: PDB / ID: 8eav
TitleYAR027W and YAR028W in complex with c subunits from yeast VO complex
Components
  • (YAR027W or YAR028W) x 9
  • (subunit from the c ring of yeast VO ...) x 2
KeywordsMEMBRANE PROTEIN / V-type / ATPase / assembly / proton
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.7 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
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YAR027W or YAR028W
Q: YAR027W or YAR028W
K: YAR027W or YAR028W
L: YAR027W or YAR028W
k: subunit from the c ring of yeast VO complex
M: subunit from the c ring of yeast VO complex
B: subunit from the c ring of yeast VO complex
C: subunit from the c ring of yeast VO complex
D: subunit from the c ring of yeast VO complex
E: subunit from the c ring of yeast VO complex
F: subunit from the c ring of yeast VO complex
G: subunit from the c ring of yeast VO complex
H: subunit from the c ring of yeast VO complex
I: YAR027W or YAR028W
J: YAR027W or YAR028W
N: YAR027W or YAR028W
O: YAR027W or YAR028W
P: YAR027W or YAR028W


Theoretical massNumber of molelcules
Total (without water)246,27718
Polymers246,27718
Non-polymers00
Water0
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 , 9 types, 9 molecules AQKLIJNOP

#1: Protein YAR027W or YAR028W


Mass: 11762.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#2: Protein YAR027W or YAR028W


Mass: 15166.669 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#3: Protein YAR027W or YAR028W


Mass: 14656.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#4: Protein YAR027W or YAR028W


Mass: 14315.630 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#7: Protein YAR027W or YAR028W


Mass: 15932.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#8: Protein YAR027W or YAR028W


Mass: 13805.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#9: Protein YAR027W or YAR028W


Mass: 15081.565 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#10: Protein YAR027W or YAR028W


Mass: 13294.380 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#11: Protein YAR027W or YAR028W


Mass: 11507.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

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Subunit from the c ring of yeast VO ... , 2 types, 9 molecules kMBCDEFGH

#5: Protein subunit from the c ring of yeast VO complex


Mass: 12358.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#6: Protein
subunit from the c ring of yeast VO complex


Mass: 13549.694 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

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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: YAR027W and YAR028W in complex with c subunits from yeast VO complex
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
VitrificationCryogen 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 FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 49 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19849 / Symmetry type: POINT

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