7ZTY | pdb_00007zty

Structure of Vps39 N-terminal domain from Chaetomium thermophilum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 
    0.298 (Depositor), 0.305 (DCC) 
  • R-Value Work: 
    0.269 (Depositor), 0.269 (DCC) 
  • R-Value Observed: 
    0.270 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 7ZTY

This is version 1.3 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: 54.94 kDa 
  • Atom Count: 2,691 
  • Modeled Residue Count: 345 
  • Deposited Residue Count: 502 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CNH domain-containing protein502Thermochaetoides thermophilaMutation(s): 0 
Gene Names: CTHT_0004950
UniProt
Find proteins for G0RY05 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0RY05 
Go to UniProtKB:  G0RY05
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0RY05
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free:  0.298 (Depositor), 0.305 (DCC) 
  • R-Value Work:  0.269 (Depositor), 0.269 (DCC) 
  • R-Value Observed: 0.270 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.7α = 90
b = 102.75β = 90
c = 59.56γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFP944-P17

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-21
    Type: Initial release
  • Version 1.1: 2022-09-28
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary