8HF3

Cryo-EM structure of human ZDHHC9/GCP16 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Regulation of RAS palmitoyltransferases by accessory proteins and palmitoylation.

Yang, A.Liu, S.Zhang, Y.Chen, J.Fan, Y.Wang, F.Zou, Y.Feng, S.Wu, J.Hu, Q.

(2024) Nat Struct Mol Biol 31: 436-446

  • DOI: https://doi.org/10.1038/s41594-023-01183-5
  • Primary Citation of Related Structures:  
    8HF3, 8HFC

  • PubMed Abstract: 

    Palmitoylation of cysteine residues at the C-terminal hypervariable regions in human HRAS and NRAS, which is necessary for RAS signaling, is catalyzed by the acyltransferase DHHC9 in complex with its accessory protein GCP16. The molecular basis for the acyltransferase activity and the regulation of DHHC9 by GCP16 is not clear. Here we report the cryo-electron microscopy structures of the human DHHC9-GCP16 complex and its yeast counterpart-the Erf2-Erf4 complex, demonstrating that GCP16 and Erf4 are not directly involved in the catalytic process but stabilize the architecture of DHHC9 and Erf2, respectively. We found that a phospholipid binding to an arginine-rich region of DHHC9 and palmitoylation on three residues (C24, C25 and C288) were essential for the catalytic activity of the DHHC9-GCP16 complex. Moreover, we showed that GCP16 also formed complexes with DHHC14 and DHHC18 to catalyze RAS palmitoylation. These findings provide insights into the regulatory mechanism of RAS palmitoyltransferases.


  • Organizational Affiliation

    College of Life Sciences, Zhejiang University, Hangzhou, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Palmitoyltransferase ZDHHC9372Homo sapiensMutation(s): 0 
Gene Names: ZDHHC9CXorf11ZDHHC10ZNF379ZNF380CGI-89UNQ261/PRO298
EC: 2.3.1.225
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y397 (Homo sapiens)
Explore Q9Y397 
Go to UniProtKB:  Q9Y397
PHAROS:  Q9Y397
GTEx:  ENSG00000188706 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y397
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Golgin subfamily A member 7144Homo 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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-22
    Type: Initial release
  • Version 1.1: 2024-06-05
    Changes: Database references