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- PDB-9cop: Yeast RAVE bound to V-ATPase V1 complex -

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Basic information

Entry
Database: PDB / ID: 9cop
TitleYeast RAVE bound to V-ATPase V1 complex
Components
  • (Regulator of V-ATPase in vacuolar membrane protein ...) x 2
  • (V-type proton ATPase subunit ...) x 6
  • Suppressor of kinetochore protein 1
  • V-type proton ATPase catalytic subunit A
KeywordsHYDROLASE / V-ATPase / RAVE / assembly
Function / homology
Function and homology information


RAVE complex / Iron uptake and transport / CBF3 complex / regulation of transcription by galactose / regulation of sulfur amino acid metabolic process / cellular response to methylmercury / vacuolar proton-transporting V-type ATPase complex assembly / vacuole-mitochondrion membrane contact site / septin ring assembly / Insulin receptor recycling ...RAVE complex / Iron uptake and transport / CBF3 complex / regulation of transcription by galactose / regulation of sulfur amino acid metabolic process / cellular response to methylmercury / vacuolar proton-transporting V-type ATPase complex assembly / vacuole-mitochondrion membrane contact site / septin ring assembly / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / proteasome storage granule assembly / vacuolar proton-transporting V-type ATPase, V1 domain / endosomal lumen acidification / regulation of exit from mitosis / proton-transporting V-type ATPase complex / kinetochore assembly / early endosome to late endosome transport / vacuolar proton-transporting V-type ATPase complex / pexophagy / intron homing / intein-mediated protein splicing / vacuolar acidification / positive regulation of D-glucose transmembrane transport / fungal-type vacuole membrane / protein neddylation / mitotic intra-S DNA damage checkpoint signaling / mitochondrial fusion / regulation of metabolic process / silent mating-type cassette heterochromatin formation / exit from mitosis / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Orc1 removal from chromatin / cullin family protein binding / Antigen processing: Ubiquitination & Proteasome degradation / DNA replication origin binding / regulation of protein-containing complex assembly / subtelomeric heterochromatin formation / ATP metabolic process / H+-transporting two-sector ATPase / negative regulation of cytoplasmic translation / proton-transporting ATPase activity, rotational mechanism / Neutrophil degranulation / proton-transporting ATP synthase activity, rotational mechanism / endomembrane system / proton transmembrane transport / regulation of mitotic cell cycle / kinetochore / transmembrane transport / G1/S transition of mitotic cell cycle / intracellular calcium ion homeostasis / cytoplasmic stress granule / G2/M transition of mitotic cell cycle / protein transport / mitotic cell cycle / protein-containing complex assembly / ubiquitin-dependent protein catabolic process / early endosome membrane / endonuclease activity / Hydrolases; Acting on ester bonds / chromosome, telomeric region / protein ubiquitination / membrane raft / Golgi membrane / mRNA binding / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / membrane / cytoplasm
Similarity search - Function
RAVE complex protein Rav1 C-terminal / : / RAVE protein 1 C terminal / RAVE subunit 2/Rogdi / Rogdi leucine zipper containing protein / Homing endonuclease PI-Sce / Homing endonuclease / Hom-end-associated Hint / Hom_end-associated Hint / ATPase, V1 complex, subunit H ...RAVE complex protein Rav1 C-terminal / : / RAVE protein 1 C terminal / RAVE subunit 2/Rogdi / Rogdi leucine zipper containing protein / Homing endonuclease PI-Sce / Homing endonuclease / Hom-end-associated Hint / Hom_end-associated Hint / 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 / Vacuolar (H+)-ATPase G subunit / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit B / Intein / ATPase, V1 complex, subunit F, eukaryotic / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / ATPase, V1 complex, subunit D / V-type ATPase subunit E / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase subunit D / ATP synthase (F/14-kDa) subunit / ATP synthase (E/31 kDa) subunit / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Homing endonuclease / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / V-type ATP synthase regulatory subunit B/beta / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit barrel-sandwich domain / Hint domain superfamily / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / 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 / SKP1/BTB/POZ domain superfamily / Armadillo-like helical / Armadillo-type fold / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / V-type proton ATPase subunit B / V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit E / V-type proton ATPase subunit D / V-type proton ATPase subunit F / V-type proton ATPase subunit H / Regulator of V-ATPase in vacuolar membrane protein 1 / V-type proton ATPase subunit G / Suppressor of kinetochore protein 1 / Regulator of V-ATPase in vacuolar membrane protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsWang, H. / Rubinstein, J.L.
Funding support United States, Canada, 2items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)1R35GM145256 United States
Canadian Institutes of Health Research (CIHR)PJT166152 Canada
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Structure of yeast RAVE bound to a partial V complex.
Authors: Hanlin Wang / Maureen Tarsio / Patricia M Kane / John L Rubinstein /
Abstract: Vacuolar-type ATPases (V-ATPases) are membrane-embedded proton pumps that acidify intracellular compartments in almost all eukaryotic cells. Homologous with ATP synthases, these multisubunit enzymes ...Vacuolar-type ATPases (V-ATPases) are membrane-embedded proton pumps that acidify intracellular compartments in almost all eukaryotic cells. Homologous with ATP synthases, these multisubunit enzymes consist of a soluble catalytic V subcomplex and a membrane-embedded proton-translocating V subcomplex. The V and V subcomplexes can undergo reversible dissociation to regulate proton pumping, with reassociation of V and V requiring the protein complex known as RAVE (regulator of the ATPase of vacuoles and endosomes). In the yeast , RAVE consists of subunits Rav1p, Rav2p, and Skp1p. We used electron cryomicroscopy (cryo-EM) to determine a structure of yeast RAVE bound to V. In the structure, RAVE is an L-shaped complex with Rav2p pointing toward the membrane and Skp1p distant from both the membrane and V. Only Rav1p interacts with V, binding to a region of subunit A not found in the corresponding ATP synthase subunit. When bound to RAVE, V is in a rotational state suitable for binding the free V complex, but in the structure, it is partially disrupted, missing five of its 16 subunits. Other than these missing subunits and the conformation of the inhibitory subunit H, the V complex with RAVE appears poised for reassembly with V.
History
DepositionJul 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: V-type proton ATPase catalytic subunit A
B: V-type proton ATPase subunit B
E: V-type proton ATPase catalytic subunit A
F: V-type proton ATPase subunit B
I: V-type proton ATPase subunit E
J: V-type proton ATPase subunit G
K: V-type proton ATPase subunit E
L: V-type proton ATPase subunit G
M: V-type proton ATPase subunit D
N: V-type proton ATPase subunit F
P: V-type proton ATPase subunit H
x: Regulator of V-ATPase in vacuolar membrane protein 1
y: Regulator of V-ATPase in vacuolar membrane protein 2
z: Suppressor of kinetochore protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)747,20418
Polymers746,30114
Non-polymers9034
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 3 molecules AEz

#1: Protein V-type proton ATPase catalytic subunit A / V-ATPase subunit A / Vacuolar proton pump subunit A


Mass: 118782.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P17255, H+-transporting two-sector ATPase
#10: Protein Suppressor of kinetochore protein 1 / Centromere DNA-binding protein complex CBF3 subunit D / E3 ubiquitin ligase complex SCF subunit SKP1


Mass: 22357.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P52286

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V-type proton ATPase subunit ... , 6 types, 9 molecules BFIKJLMNP

#2: Protein V-type proton ATPase subunit B / V-ATPase subunit B / V-ATPase 57 kDa subunit / Vacuolar proton pump subunit B


Mass: 57815.023 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P16140
#3: Protein V-type proton ATPase subunit E / V-ATPase subunit E / V-ATPase 27 kDa subunit / Vacuolar proton pump subunit E


Mass: 26508.393 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22203
#4: Protein V-type proton ATPase subunit G / V-ATPase subunit G / V-ATPase 13 kDa subunit / Vacuolar proton pump subunit G


Mass: 12738.706 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P48836
#5: Protein V-type proton ATPase subunit D / V-ATPase subunit D / Vacuolar proton pump subunit D


Mass: 29235.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32610
#6: Protein V-type proton ATPase subunit F / V-ATPase subunit F / V-ATPase 14 kDa subunit / Vacuolar proton pump subunit F


Mass: 13347.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39111
#7: 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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Regulator of V-ATPase in vacuolar membrane protein ... , 2 types, 2 molecules xy

#8: Protein Regulator of V-ATPase in vacuolar membrane protein 1 / Suppression of the onset of impotence protein 3


Mass: 155127.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P47104
#9: Protein Regulator of V-ATPase in vacuolar membrane protein 2


Mass: 40061.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03956

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Non-polymers , 2 types, 4 molecules

#11: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / 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
Has protein modificationN

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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 RAVE bound to V-ATPase V1 complex / Type: COMPLEX / Entity ID: #1-#10 / 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

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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: 2300 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 42 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71341 / Symmetry type: POINT

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