6JWP

crystal structure of EGOC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.233 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural insights into the EGO-TC-mediated membrane tethering of the TORC1-regulatory Rag GTPases.

Zhang, T.Peli-Gulli, M.P.Zhang, Z.Tang, X.Ye, J.De Virgilio, C.Ding, J.

(2019) Sci Adv 5: eaax8164-eaax8164

  • DOI: https://doi.org/10.1126/sciadv.aax8164
  • Primary Citation of Related Structures:  
    6JWP

  • PubMed Abstract: 

    The Rag/Gtr GTPases serve as a central module in the nutrient-sensing signaling network upstream of TORC1. In yeast, the anchoring of Gtr1-Gtr2 to membranes depends on the Ego1-Ego2-Ego3 ternary complex (EGO-TC), resulting in an EGO-TC-Gtr1-Gtr2 complex (EGOC). EGO-TC and human Ragulator share no obvious sequence similarities and also differ in their composition with respect to the number of known subunits, which raises the question of how the EGO-TC fulfills its function in recruiting Gtr1-Gtr2. Here, we report the structure of EGOC, in which Ego1 wraps around Ego2, Ego3, and Gtr1-Gtr2. In addition, Ego3 interacts with Gtr1-Gtr2 to stabilize the complex. The functional roles of key residues involved in the assembly are validated by in vivo assays. Our structural and functional data combined demonstrate that EGOC and Ragulator-Rag complex are structurally conserved and that EGO-TC is essential and sufficient to recruit Gtr1-Gtr2 to membranes to ensure appropriate TORC1 signaling.


  • Organizational Affiliation

    State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding protein GTR1
A, F
312Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: GTR1
UniProt
Find proteins for Q00582 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q00582 
Go to UniProtKB:  Q00582
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00582
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding protein GTR2
B, G
345Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: GTR2
UniProt
Find proteins for P53290 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53290 
Go to UniProtKB:  P53290
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53290
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein MEH1
C, H
129Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q02205 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02205 
Go to UniProtKB:  Q02205
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02205
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ego2
D, I
75Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: Gtr2
UniProt
Find proteins for Q3E830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q3E830 
Go to UniProtKB:  Q3E830
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3E830
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SLM4
E, J
162Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: EGO3
UniProt
Find proteins for P38247 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38247 
Go to UniProtKB:  P38247
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38247
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.233 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.675α = 90
b = 120.547β = 90
c = 323.274γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description