9OA6 | pdb_00009oa6

Cryo-EM structure of the Zdhhc5-GOLGA7 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Functional dissection of the zDHHC palmitoyltransferase 5-golgin A7 palmitoylation complex.

Kahlson, M.A.Ritho, J.Gomes, J.V.Wang, H.Butterwick, J.A.Dixon, S.J.

(2025) J Biological Chem 301: 110694-110694

  • DOI: https://doi.org/10.1016/j.jbc.2025.110694
  • Primary Citation of Related Structures:  
    9OA6

  • PubMed Abstract: 

    Small molecules serve as valuable tools for probing nonapoptotic cell death mechanisms. The small molecule caspase independent lethal 56 (CIL56) induces a unique form of nonapoptotic cancer cell death that is promoted by a complex formed between zDHHC palmitoyltransferase 5 (ZDHHC5) and an accessory protein, golgin A7 (GOLGA7, also known as GCP16). The structure and function of this complex in nonapoptotic cell death regulation remain poorly understood. Here, we use coimmunoprecipitation, functional assays, and cryogenic electron microscopy (cryo-EM) to elucidate the structure and function of the Zdhhc5-GOLGA7 complex. We identify key residues in both Zdhhc5 and GOLGA7 that are necessary for complex formation and to promote nonapoptotic cancer cell death in response to caspase independent lethal 56. These results provide new insights into the structure and function of a death-promoting protein complex.


  • Organizational Affiliation
    • Department of Biology, Stanford University, Stanford, California, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Golgin subfamily A member 7A [auth B]153Homo sapiensMutation(s): 0 
Gene Names: GOLGA7GCP16HDCKB03PHSPC041
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z5G4 (Homo sapiens)
Explore Q7Z5G4 
Go to UniProtKB:  Q7Z5G4
PHAROS:  Q7Z5G4
GTEx:  ENSG00000147533 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z5G4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Palmitoyltransferase ZDHHC5B [auth A]718Mus musculusMutation(s): 0 
Gene Names: Zdhhc5Kiaa1748
EC: 2.3.1.225
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8VDZ4 (Mus musculus)
Explore Q8VDZ4 
Go to UniProtKB:  Q8VDZ4
IMPC:  MGI:1923573
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8VDZ4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419:
RECONSTRUCTIONcryoSPARC4.3

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA272485
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM007276

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-22
    Type: Initial release