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- EMDB-14965: HOPS tethering complex from yeast, consensus map covering the upp... -

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Entry
Database: EMDB / ID: EMD-14965
TitleHOPS tethering complex from yeast, consensus map covering the upper part of the complex
Map dataTethering complex HOPS; consensus map covering the upper part of the complex
Sample
  • Complex: Tethering complex HOPS
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 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_14965.png

Downloads & links

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Map

FileDownload / File: emd_14965.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTethering complex HOPS; consensus map covering the upper part of the complex
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: 0.15
Minimum - Maximum-0.37645644 - 0.70360166
Average (Standard dev.)-0.00029629783 (±0.009162527)
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; consensus map covering the upper...

Fileemd_14965_half_map_1.map
AnnotationTethering complex HOPS; consensus map covering the upper part of the complex - Half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Tethering complex HOPS; consensus map covering the upper...

Fileemd_14965_half_map_2.map
AnnotationTethering complex HOPS; consensus map covering the upper part of the complex - Half map B
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: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 129389
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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