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- PDB-8qx8: Endosomal membrane tethering complex CORVET -

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Basic information

Entry
Database: PDB / ID: 8qx8
TitleEndosomal membrane tethering complex CORVET
Components
  • (Vacuolar protein sorting-associated protein ...) x 4
  • E3 ubiquitin-protein ligase PEP5
  • Vacuolar membrane protein PEP3
KeywordsENDOCYTOSIS / CORVET / membrane fusion / endosome / Rab GTPase / tethering
Function / homology
Function and homology information


histone catabolic process / organelle fusion / CORVET complex / regulation of SNARE complex assembly / HOPS complex / endosomal vesicle fusion / vesicle tethering / regulation of vacuole fusion, non-autophagic / vacuole fusion, non-autophagic / Golgi to vacuole transport ...histone catabolic process / organelle fusion / CORVET complex / regulation of SNARE complex assembly / HOPS complex / endosomal vesicle fusion / vesicle tethering / regulation of vacuole fusion, non-autophagic / vacuole fusion, non-autophagic / Golgi to vacuole transport / vacuole inheritance / Golgi to endosome transport / vesicle fusion with vacuole / vesicle docking / late endosome to vacuole transport via multivesicular body sorting pathway / endosome organization / vacuole organization / protein targeting to vacuole / Golgi stack / late endosome to vacuole transport / fungal-type vacuole / piecemeal microautophagy of the nucleus / vacuolar acidification / fungal-type vacuole membrane / vesicle docking involved in exocytosis / endosomal transport / protein-membrane adaptor activity / vesicle-mediated transport / intracellular protein transport / RING-type E3 ubiquitin transferase / autophagy / endocytosis / ubiquitin protein ligase activity / late endosome / actin binding / GTPase binding / early endosome membrane / protein-macromolecule adaptor activity / endosome / ATP binding / membrane / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Vacuolar protein sorting-associated protein 8, central domain / Vps8 central TPR / Vacuolar protein sorting-associated protein Vps41/Vps8 / Pep3/Vps18/deep orange / Vacuolar protein sorting-associated protein 11 / Vacuolar protein sorting protein 11, C-terminal / Pep3/Vps18/deep orange beta-propeller domain / Vacuolar protein sorting protein 11 C terminal / Vam6/VPS39/TRAP1 family / Vps16, C-terminal ...Vacuolar protein sorting-associated protein 8, central domain / Vps8 central TPR / Vacuolar protein sorting-associated protein Vps41/Vps8 / Pep3/Vps18/deep orange / Vacuolar protein sorting-associated protein 11 / Vacuolar protein sorting protein 11, C-terminal / Pep3/Vps18/deep orange beta-propeller domain / Vacuolar protein sorting protein 11 C terminal / Vam6/VPS39/TRAP1 family / Vps16, C-terminal / Vps16, N-terminal / Vacuolar protein sorting-associated protein 16 / Vps16, C-terminal domain superfamily / Vps16, C-terminal region / Vps16, N-terminal region / Vacuolar protein sorting-associated protein 33, domain 3b / Sec1-like protein / Sec1-like, domain 2 / Sec1-like superfamily / Sec1-like, domain 3a / Sec1 family / Clathrin heavy chain repeat homology / Clathrin, heavy chain/VPS, 7-fold repeat / Clathrin heavy-chain (CHCR) repeat profile. / Citron homology (CNH) domain / Citron homology (CNH) domain profile. / Ring finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase PEP5 / Vacuolar protein sorting-associated protein 33 / Vacuolar protein sorting-associated protein 3 / Vacuolar membrane protein PEP3 / Vacuolar protein sorting-associated protein 8 / Vacuolar protein sorting-associated protein 16
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsShvarev, D. / Ungermann, C. / Moeller, A.
Funding support Germany, 6items
OrganizationGrant numberCountry
German Research Foundation (DFG)UN111/5-6 Germany
German Research Foundation (DFG)MO2752/3-6 Germany
German Research Foundation (DFG)SFB 944 Germany
German Research Foundation (DFG)SFB 1557 Germany
German Research Foundation (DFG)INST190/196-1 FUGG Germany
German Federal Ministry for Education and ResearchDLR 01ED2010 Germany
CitationJournal: Nat Commun / Year: 2024
Title: Structure of the endosomal CORVET tethering complex.
Authors: Dmitry Shvarev / Caroline König / Nicole Susan / Lars Langemeyer / Stefan Walter / Angela Perz / Florian Fröhlich / Christian Ungermann / Arne Moeller /
Abstract: Cells depend on their endolysosomal system for nutrient uptake and downregulation of plasma membrane proteins. These processes rely on endosomal maturation, which requires multiple membrane fusion ...Cells depend on their endolysosomal system for nutrient uptake and downregulation of plasma membrane proteins. These processes rely on endosomal maturation, which requires multiple membrane fusion steps. Early endosome fusion is promoted by the Rab5 GTPase and its effector, the hexameric CORVET tethering complex, which is homologous to the lysosomal HOPS. How these related complexes recognize their specific target membranes remains entirely elusive. Here, we solve the structure of CORVET by cryo-electron microscopy and revealed its minimal requirements for membrane tethering. As expected, the core of CORVET and HOPS resembles each other. However, the function-defining subunits show marked structural differences. Notably, we discover that unlike HOPS, CORVET depends not only on Rab5 but also on phosphatidylinositol-3-phosphate (PI3P) and membrane lipid packing defects for tethering, implying that an organelle-specific membrane code enables fusion. Our data suggest that both shape and membrane interactions of CORVET and HOPS are conserved in metazoans, thus providing a paradigm how tethering complexes function.
History
DepositionOct 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Vacuolar protein sorting-associated protein 8
D: Vacuolar protein sorting-associated protein 33
B: Vacuolar protein sorting-associated protein 16
A: E3 ubiquitin-protein ligase PEP5
E: Vacuolar protein sorting-associated protein 3
C: Vacuolar membrane protein PEP3


Theoretical massNumber of molelcules
Total (without water)662,5316
Polymers662,5316
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Vacuolar protein sorting-associated protein ... , 4 types, 4 molecules FDBE

#1: Protein Vacuolar protein sorting-associated protein 8 / Vacuolar protein-targeting protein 8


Mass: 148102.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VPS8, VPT8, YAL002W, FUN15 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39702
#2: Protein Vacuolar protein sorting-associated protein 33 / Protein SLP1 / Vacuolar morphogenesis protein 5


Mass: 79354.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VPS33, SLP1, VAM5, YLR396C, L8084.15 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20795
#3: Protein Vacuolar protein sorting-associated protein 16 / Vacuolar morphogenesis protein 9 / Vacuolar protein-targeting protein 16


Mass: 92857.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VPS16, VAM9, VPT16, YPL045W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03308
#5: Protein Vacuolar protein sorting-associated protein 3 / Vacuolar protein-targeting protein 17


Mass: 117069.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VPS3, VPT17, YDR495C, D9719.1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23643

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Protein , 2 types, 2 molecules AC

#4: Protein E3 ubiquitin-protein ligase PEP5 / Carboxypeptidase Y-deficient protein 5 / Histone E3 ligase PEP5 / RING-type E3 ubiquitin ...Carboxypeptidase Y-deficient protein 5 / Histone E3 ligase PEP5 / RING-type E3 ubiquitin transferase PEP5 / Vacuolar biogenesis protein END1 / Vacuolar morphogenesis protein 1 / Vacuolar protein sorting-associated protein 11 / Vacuolar protein-targeting protein 11


Mass: 117617.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PEP5, END1, VAM1, VPL9, VPS11, VPT11, YMR231W, YM9959.13
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P12868, RING-type E3 ubiquitin transferase
#6: Protein Vacuolar membrane protein PEP3 / Carboxypeptidase Y-deficient protein 3 / Vacuolar morphogenesis protein 8 / Vacuolar protein ...Carboxypeptidase Y-deficient protein 3 / Vacuolar morphogenesis protein 8 / Vacuolar protein sorting-associated protein 18 / Vacuolar protein-targeting protein 18


Mass: 107531.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PEP3, VAM8, VPS18, VPT18, YLR148W, L9634.2 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P27801

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Details

Has protein modificationY

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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: Endosomal membrane tethering complex CORVET / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 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: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 219391 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00230592
ELECTRON MICROSCOPYf_angle_d0.50741762
ELECTRON MICROSCOPYf_dihedral_angle_d4.0124605
ELECTRON MICROSCOPYf_chiral_restr0.045160
ELECTRON MICROSCOPYf_plane_restr0.0035489

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