7E2M

Crystal structure of the RWD domain of human GCN2 - 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 

Starting Model: experimental
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Literature

Crystal structures reveal a novel dimer of the RWD domain of human general control nonderepressible 2.

Hei, Z.Wu, S.Zheng, L.Zhou, J.Liu, Z.Wang, J.Fang, P.

(2021) Biochem Biophys Res Commun 549: 164-170

  • DOI: https://doi.org/10.1016/j.bbrc.2021.02.111
  • Primary Citation of Related Structures:  
    7E2K, 7E2M

  • PubMed Abstract: 

    General control nonderepressible 2 (GCN2) is a serine/threonine protein kinase, detecting a variety of stresses including amino acid starvation, reactive oxygen species, etc. in eukaryotic cells. Activation of GCN2 requires the interaction of the N-terminal RWD domain with the upstream GCN1 protein and the dimerization by the kinase domain. In this study, we determined two crystal structures of the RWD domain of human GCN2 in two different crystal packing modes. These two different crystal structures reveal a same dimer of the RWD domain, which has not been reported in previous studies. We further confirmed this novel dimer interaction in solution using gel filtration experiments, and in human embryonic kidney (HEK) 293 cells using bimolecular fluorescence complementation (BiFC) and co-immunoprecipitation (co-IP) assays. Together, this study discovers a potential protein-protein interface on the RWD domain of human GCN2, and suggests a possible regulation between the interaction of GCN1 and the formation of GCN2 dimer.


  • Organizational Affiliation

    State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
eIF-2-alpha kinase GCN2
A, B, C, D, E
A, B, C, D, E, F
135Homo sapiensMutation(s): 0 
Gene Names: EIF2AK4GCN2KIAA1338
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P2K8 (Homo sapiens)
Explore Q9P2K8 
Go to UniProtKB:  Q9P2K8
PHAROS:  Q9P2K8
GTEx:  ENSG00000128829 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P2K8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.44α = 90
b = 158.44β = 90
c = 54.5γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21778064
National Natural Science Foundation of China (NSFC)China21977107

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-17
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description