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Open data
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Basic information
Entry | Database: PDB / ID: 8qx8 | |||||||||||||||||||||
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Title | Endosomal membrane tethering complex CORVET | |||||||||||||||||||||
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![]() | ENDOCYTOSIS / CORVET / membrane fusion / endosome / Rab GTPase / tethering | |||||||||||||||||||||
Function / homology | ![]() histone catabolic process / organelle fusion / endosomal vesicle fusion / regulation of SNARE complex assembly / CORVET complex / HOPS complex / vesicle tethering / regulation of vacuole fusion, non-autophagic / vacuole inheritance / vacuole fusion, non-autophagic ...histone catabolic process / organelle fusion / endosomal vesicle fusion / regulation of SNARE complex assembly / CORVET complex / HOPS complex / vesicle tethering / regulation of vacuole fusion, non-autophagic / vacuole inheritance / vacuole fusion, non-autophagic / vesicle fusion with vacuole / Golgi to endosome transport / Golgi to vacuole transport / vesicle docking / late endosome to vacuole transport via multivesicular body sorting pathway / endosome organization / vacuole organization / protein targeting to vacuole / late endosome to vacuole transport / piecemeal microautophagy of the nucleus / Golgi stack / fungal-type vacuole / fungal-type vacuole membrane / vesicle docking involved in exocytosis / vacuolar acidification / endosomal transport / lysosome organization / endosome to lysosome transport / protein-membrane adaptor activity / vesicle-mediated transport / intracellular protein transport / RING-type E3 ubiquitin transferase / autophagy / endocytosis / ubiquitin protein ligase activity / late endosome / GTPase binding / protein-macromolecule adaptor activity / actin binding / early endosome membrane / endosome / ATP binding / membrane / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å | |||||||||||||||||||||
![]() | Shvarev, D. / Ungermann, C. / Moeller, A. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 752.6 KB | Display | ![]() |
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PDB format | ![]() | 562.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 808 KB | Display | ![]() |
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Full document | ![]() | 844.1 KB | Display | |
Data in XML | ![]() | 100.7 KB | Display | |
Data in CIF | ![]() | 161.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 18701MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Vacuolar protein sorting-associated protein ... , 4 types, 4 molecules FDBE
#1: Protein | Mass: 148102.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: VPS8, VPT8, YAL002W, FUN15 / Production host: ![]() ![]() |
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#2: Protein | Mass: 79354.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: VPS33, SLP1, VAM5, YLR396C, L8084.15 / Production host: ![]() ![]() |
#3: Protein | Mass: 92857.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: VPS16, VAM9, VPT16, YPL045W / Production host: ![]() ![]() |
#5: Protein | Mass: 117069.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: VPS3, VPT17, YDR495C, D9719.1 / Production host: ![]() ![]() |
-Protein , 2 types, 2 molecules AC
#4: Protein | Mass: 117617.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PEP5, END1, VAM1, VPL9, VPS11, VPT11, YMR231W, YM9959.13 Production host: ![]() ![]() References: UniProt: P12868, RING-type E3 ubiquitin transferase |
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#6: Protein | Mass: 107531.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PEP3, VAM8, VPS18, VPT18, YLR148W, L9634.2 / Production host: ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Endosomal membrane tethering complex CORVET / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
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Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 219391 / Symmetry type: POINT | ||||||||||||||||||||||||
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