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- EMDB-14970: HOPS tethering complex from yeast, local refinement map of the bo... -

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Basic information

Entry
Database: EMDB / ID: EMD-14970
TitleHOPS tethering complex from yeast, local refinement map of the bottom part of the complex (Vps39)
Map dataTethering complex HOPS, local refinement map of the bottom part of the complex (Vps39)
Sample
  • Complex: Tethering complex HOPS
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.0 Å
AuthorsShvarev D / Schoppe J / Koenig C / Perz A / Fuellbrunn N / Kiontke S / Langemeyer L / Januliene D / Schnelle K / Kuemmel D ...Shvarev D / Schoppe J / Koenig C / Perz A / Fuellbrunn N / Kiontke S / Langemeyer L / Januliene D / Schnelle K / Kuemmel D / Froehlich F / Moeller A / Ungermann C
Funding support Germany, 3 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB 944 Germany
German Research Foundation (DFG)INST190/196-1 FUGG Germany
German Federal Ministry for Education and ResearchDLR 01ED2010 Germany
CitationJournal: Elife / Year: 2022
Title: Structure of the HOPS tethering complex, a lysosomal membrane fusion machinery.
Authors: Dmitry Shvarev / Jannis Schoppe / Caroline König / Angela Perz / Nadia Füllbrunn / Stephan Kiontke / Lars Langemeyer / Dovile Januliene / Kilian Schnelle / Daniel Kümmel / Florian ...Authors: Dmitry Shvarev / Jannis Schoppe / Caroline König / Angela Perz / Nadia Füllbrunn / Stephan Kiontke / Lars Langemeyer / Dovile Januliene / Kilian Schnelle / Daniel Kümmel / Florian Fröhlich / Arne Moeller / Christian Ungermann /
Abstract: Lysosomes are essential for cellular recycling, nutrient signaling, autophagy, and pathogenic bacteria and viruses invasion. Lysosomal fusion is fundamental to cell survival and requires HOPS, a ...Lysosomes are essential for cellular recycling, nutrient signaling, autophagy, and pathogenic bacteria and viruses invasion. Lysosomal fusion is fundamental to cell survival and requires HOPS, a conserved heterohexameric tethering complex. On the membranes to be fused, HOPS binds small membrane-associated GTPases and assembles SNAREs for fusion, but how the complex fulfills its function remained speculative. Here, we used cryo-electron microscopy to reveal the structure of HOPS. Unlike previously reported, significant flexibility of HOPS is confined to its extremities, where GTPase binding occurs. The SNARE-binding module is firmly attached to the core, therefore, ideally positioned between the membranes to catalyze fusion. Our data suggest a model for how HOPS fulfills its dual functionality of tethering and fusion and indicate why it is an essential part of the membrane fusion machinery.
History
DepositionMay 11, 2022-
Header (metadata) releaseSep 28, 2022-
Map releaseSep 28, 2022-
UpdateSep 28, 2022-
Current statusSep 28, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14970.png

Downloads & links

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Map

FileDownload / File: emd_14970.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTethering complex HOPS, local refinement map of the bottom part of the complex (Vps39)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 672 pix.
= 620.928 Å		0.92 Å/pix.
x 672 pix.
= 620.928 Å		0.92 Å/pix.
x 672 pix.
= 620.928 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.924 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-0.32759863 - 0.7503478
Average (Standard dev.)-0.00034855516 (±0.007968832)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions672672672
Spacing672672672
CellA=B=C: 620.92804 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Tethering complex HOPS, local refinement map of the...

Fileemd_14970_half_map_1.map
AnnotationTethering complex HOPS, local refinement map of the bottom part of the complex (Vps39) - half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Tethering complex HOPS, local refinement map of the...

Fileemd_14970_half_map_2.map
AnnotationTethering complex HOPS, local refinement map of the bottom part of the complex (Vps39) - 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 : Tethering complex HOPS

EntireName: Tethering complex HOPS
Components
  • Complex: Tethering complex HOPS

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Supramolecule #1: Tethering complex HOPS

SupramoleculeName: Tethering complex HOPS / type: complex / Chimera: Yes / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: 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 / Chamber humidity: 100 % / Chamber temperature: 277 K / 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: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 3.3.1)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 115272
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
FSC plot (resolution estimation)

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