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- EMDB-18702: Endosomal membrane tethering complex CORVET, Vps8-Vps11 local ref... -

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Basic information

Entry
Database: EMDB / ID: EMD-18702
TitleEndosomal membrane tethering complex CORVET, Vps8-Vps11 local refinement map
Map dataCORVET, Vps8-Vps11 local refinement map
Sample
  • Complex: Endosomal membrane tethering complex CORVET
KeywordsCORVET / membrane fusion / endosome / Rab GTPase / tethering / ENDOCYTOSIS
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsShvarev D / Koenig C / Susan N / Langemeyer L / Walter S / Perz A / Froehlich F / Ungermann C / Moeller A
Funding support Germany, 6 items
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, 2023-
Header (metadata) releaseJul 3, 2024-
Map releaseJul 3, 2024-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18702.png

Downloads & links

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Map

FileDownload / File: emd_18702.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCORVET, Vps8-Vps11 local refinement map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.59 Å/pix.
x 512 pix.
= 815.104 Å		1.59 Å/pix.
x 512 pix.
= 815.104 Å		1.59 Å/pix.
x 512 pix.
= 815.104 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.592 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.33
Minimum - Maximum-1.1975621 - 2.0586476
Average (Standard dev.)-0.00036464425 (±0.021881422)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 815.104 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: CORVET, Vps8-Vps11 local refinement half map B

Fileemd_18702_half_map_1.map
AnnotationCORVET, Vps8-Vps11 local refinement half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CORVET, Vps8-Vps11 local refinement half map A

Fileemd_18702_half_map_2.map
AnnotationCORVET, Vps8-Vps11 local refinement half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Endosomal membrane tethering complex CORVET

EntireName: Endosomal membrane tethering complex CORVET
Components
  • Complex: Endosomal membrane tethering complex CORVET

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Supramolecule #1: Endosomal membrane tethering complex CORVET

SupramoleculeName: Endosomal membrane tethering complex CORVET / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 218807
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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