5GV2

Crystal structure of Arginine-bound CASTOR1 from Homo sapiens


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural mechanism for the arginine sensing and regulation of CASTOR1 in the mTORC1 signaling pathway

Gai, Z.Wang, Q.Yang, C.Wang, L.Deng, W.Wu, G.

(2016) Cell Discov 2: 16051-16051

  • DOI: https://doi.org/10.1038/celldisc.2016.51
  • Primary Citation of Related Structures:  
    5GV2

  • PubMed Abstract: 

    The mTOR complex I (mTORC1) signaling pathway controls many metabolic processes and is regulated by amino acid signals, especially arginine. CASTOR1 has been identified as the cytosolic arginine sensor for the mTORC1 pathway, but the molecular mechanism of how it senses arginine is elusive. Here, by determining the crystal structure of human CASTOR1 in complex with arginine, we found that an exquisitely tailored pocket, carved between the NTD and the CTD domains of CASTOR1, is employed to recognize arginine. Mutation of critical residues in this pocket abolished or diminished arginine binding. By comparison with structurally similar aspartate kinases, a surface patch of CASTOR1-NTD on the opposite side of the arginine-binding site was identified to mediate direct physical interaction with its downstream effector GATOR2, via GATOR2 subunit Mios. Mutation of this surface patch disrupted CASTOR1's recognition and inhibition of GATOR2, revealed by in vitro pull-down assay. Normal mode (NM) analysis revealed an 'open'-to-'closed' conformational change for CASTOR1, which is correlated to the switching between the exposing and concealing of its GATOR2-binding residues, and is most likely related to arginine binding. Interestingly, the GATOR2-binding sites on the two protomers of CASTOR1 dimer face the same direction, which prompted us to propose a model for how dimerization of CASTOR1 relieves the inhibition of GATOR1 by GATOR2. Our study thus provides a thorough analysis on how CASTOR1 recognizes arginine, and describes a possible mechanism of how arginine binding induces the inter-domain movement of CASTOR1 to affect its association with GATOR2.


  • Organizational Affiliation

    State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University , Shanghai, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GATS-like protein 3A [auth C],
B [auth A]
349Homo sapiensMutation(s): 0 
Gene Names: GATSL3CASTOR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WTX7 (Homo sapiens)
Explore Q8WTX7 
Go to UniProtKB:  Q8WTX7
PHAROS:  Q8WTX7
GTEx:  ENSG00000239282 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WTX7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ARG
Query on ARG

Download Ideal Coordinates CCD File 
D [auth A]ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
MG
Query on MG

Download Ideal Coordinates CCD File 
C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.547α = 90
b = 76.834β = 96.21
c = 95.223γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-06
    Type: Initial release
  • Version 1.1: 2018-05-23
    Changes: Data collection
  • Version 1.2: 2019-03-20
    Changes: Data collection, Database references
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references