4XPM

Crystal structure of EGO-TC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the Ego1-Ego2-Ego3 complex and its role in promoting Rag GTPase-dependent TORC1 signaling.

Powis, K.Zhang, T.Panchaud, N.Wang, R.De Virgilio, C.Ding, J.

(2015) Cell Res 25: 1043-1059

  • DOI: https://doi.org/10.1038/cr.2015.86
  • Primary Citation of Related Structures:  
    4XPM

  • PubMed Abstract: 

    The target of rapamycin complex 1 (TORC1) integrates various hormonal and nutrient signals to regulate cell growth, proliferation, and differentiation. Amino acid-dependent activation of TORC1 is mediated via the yeast EGO complex (EGOC) consisting of Gtr1, Gtr2, Ego1, and Ego3. Here, we identify the previously uncharacterized Ycr075w-a/Ego2 protein as an additional EGOC component that is required for the integrity and localization of the heterodimeric Gtr1-Gtr2 GTPases, equivalent to mammalian Rag GTPases. We also report the crystal structure of the Ego1-Ego2-Ego3 ternary complex (EGO-TC) at 2.4 Å resolution, in which Ego2 and Ego3 form a heterodimer flanked along one side by Ego1. Structural data also reveal the structural conservation of protein components between the yeast EGO-TC and the human Ragulator, which acts as a GEF for Rag GTPases. Interestingly, however, artificial tethering of Gtr1-Gtr2 to the vacuolar membrane is sufficient to activate TORC1 in response to amino acids even in the absence of the EGO-TC. Our structural and functional data therefore support a model in which the EGO-TC acts as a scaffold for Rag GTPases in TORC1 signaling.


  • Organizational Affiliation

    Department of Biology, University of Fribourg, Fribourg CH-1700, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein MEH139Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MEH1EGO1GSE2YKR007WYK106
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
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein YCR075W-A76Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YCR075W-A
UniProt
Find proteins for Q3E830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q3E830 
Go to UniProtKB:  Q3E830
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UniProt GroupQ3E830
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SLM4162Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SLM4EGO3GSE1YBR077CYBR0723
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.118α = 90
b = 48.118β = 90
c = 223.377γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-10-14
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description