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 7ZU0 | pdb_00007zu0

HOPS tethering complex from yeast


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7ZU0

This is version 1.4 of the entry. See complete history. 

Literature

Structure of the HOPS tethering complex, a lysosomal membrane fusion machinery.

Shvarev, D., Schoppe, J., Konig, C., Perz, A., Fullbrunn, N., Kiontke, S., Langemeyer, L., Januliene, D., Schnelle, K., Kummel, D., Frohlich, F., Moeller, A., Ungermann, C.

(2022) Elife 11

  • DOI: https://doi.org/10.7554/eLife.80901
  • Primary Citation Related Structures: 
    7ZTY, 7ZU0

  • PubMed 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 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.


  • Organizational Affiliation: 
    • Department of Biology/Chemistry, Structural Biology section, Osnabrück University, Osnabrück, Germany.

Macromolecule Content 

  • Total Structure Weight: 636.94 kDa 
  • Atom Count: 25,763 
  • Modeled Residue Count: 3,581 
  • Deposited Residue Count: 5,501 
  • Unique protein chains: 6

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase PEP51,029Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PEP5, END1, VAM1, VPL9, VPS11, VPT11, YMR231W, YM9959.13
EC: 2.3.2.27
UniProt
Find proteins for P12868 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P12868 
Go to UniProtKB:  P12868
Entity Groups
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UniProt GroupP12868
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 16798Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: VPS16, VAM9, VPT16, YPL045W
UniProt
Find proteins for Q03308 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03308 
Go to UniProtKB:  Q03308
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UniProt GroupQ03308
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Vacuolar membrane protein PEP3918Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PEP3, VAM8, VPS18, VPT18, YLR148W, L9634.2
UniProt
Find proteins for P27801 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P27801 
Go to UniProtKB:  P27801
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UniProt GroupP27801
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 33691Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: VPS33, SLP1, VAM5, YLR396C, L8084.15
UniProt
Find proteins for P20795 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20795 
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UniProt GroupP20795
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Vacuolar morphogenesis protein 61,049Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: VAM6, CVT4, VPL18, VPL22, VPS39, YDL077C
UniProt
Find proteins for Q07468 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupQ07468
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 411,016Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: VPS41, FET2, VAM2, YDR080W, D446, YD8554.13
UniProt
Find proteins for P38959 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38959 
Go to UniProtKB:  P38959
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UniProt GroupP38959
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB 944
German Research Foundation (DFG)GermanyINST190/196-1 FUGG
German Federal Ministry for Education and ResearchGermanyDLR 01ED2010

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-28
    Type: Initial release
  • Version 1.1: 2022-10-05
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2022-10-12
    Changes: Database references
  • Version 1.3: 2024-07-24
    Changes: Data collection, Database references
  • Version 1.4: 2025-04-16
    Changes: Data collection, Database references, Structure summary