8DIT | pdb_00008dit

Cryo-EM structure of a HOPS core complex containing Vps33, Vps16, and Vps18

• PDB DOI: https://doi.org/10.2210/pdb8DIT/pdb
• EM Map EMD-27442: EMDB EMDataResource

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


• Deposited: 2022-06-29 Released: 2022-08-31 
• Deposition Author(s): Port, S.A., Farrell, P.D., Jeffrey, P.D., DiMaio, F., Hughson, F.M.
• Funding Organization(s): German Research Foundation (DFG), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 5.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of the HOPS core complex and its implication for SNARE assembly

Port, S.A., Farrell, P.D., Jeffrey, P.D., DiMaio, F., Hughson, F.M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 279.85 kDa 
• Atom Count: 17,303 
• Modeled Residue Count: 2,190 
• Deposited Residue Count: 2,498 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar protein sorting-associated protein 33	A	696	Thermochaetoides thermophila	Mutation(s): 0
UniProt
Find proteins for G0SCM5 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0SCM5  Go to UniProtKB:  G0SCM5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar protein sorting-associated protein 16	B	834	Thermochaetoides thermophila	Mutation(s): 0
UniProt
Find proteins for G0S6M7 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0S6M7  Go to UniProtKB:  G0S6M7

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar protein sorting-associated protein 18	C	968	Thermochaetoides thermophila	Mutation(s): 0
UniProt
Find proteins for G0S4R9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0S4R9  Go to UniProtKB:  G0S4R9

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 5.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	2.15.0
RECONSTRUCTION	RELION	3.1.0

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-08-31 
Deposition Author(s): Port, S.A., Farrell, P.D., Jeffrey, P.D., DiMaio, F., Hughson, F.M.

---

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	PO2195/1-1
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM071574
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM123089

Revision History  

• Version 1.0: 2022-08-31
  Type: Initial release
  
• Version 1.1: 2024-02-14
  Changes: Data collection