7ZTY

Structure of Vps39 N-terminal domain from Chaetomium thermophilum

• PDB DOI: https://doi.org/10.2210/pdb7ZTY/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Thermochaetoides thermophila
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-05-11 Released: 2022-09-21 
• Deposition Author(s): Kiontke, S., Ungermann, C., Kuemmel, D.
• Funding Organization(s): German Research Foundation (DFG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 0.298 
• R-Value Work: 0.269 
• R-Value Observed: 0.270 

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

• PubMed: 36098503 
• DOI: https://doi.org/10.7554/eLife.80901
• Primary Citation of 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 54.94 kDa 
• Atom Count: 2,691 
• Modelled Residue Count: 345 
• Deposited Residue Count: 502 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CNH domain-containing protein	A	502	Thermochaetoides thermophila	Mutation(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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 0.298 
• R-Value Work: 0.269 
• R-Value Observed: 0.270 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.7	α = 90
b = 102.75	β = 90
c = 59.56	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-09-21 
Deposition Author(s): Kiontke, S., Ungermann, C., Kuemmel, D.

---

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SFP944-P17

Revision History  

• Version 1.0: 2022-09-21
  Type: Initial release
  
• Version 1.1: 2022-09-28
  Changes: Database references