8HFC

Cryo-EM structure of yeast Erf2/Erf4 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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 ERF2381Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ERF2YLR246W
EC: 2.3.1.225
Membrane Entity: Yes 
UniProt
Find proteins for Q06551 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06551 
Go to UniProtKB:  Q06551
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06551
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ras modification protein ERF4264Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SHR5ERF4YOL110WHRC237
Membrane Entity: Yes 
UniProt
Find proteins for P41912 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P41912 
Go to UniProtKB:  P41912
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41912
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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