4FTX

Crystal structure of Ego3 homodimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Ego3 functions as a homodimer to mediate the interaction between Gtr1-Gtr2 and Ego1 in the ego complex to activate TORC1.

Zhang, T.Peli-Gulli, M.P.Yang, H.De Virgilio, C.Ding, J.

(2012) Structure 20: 2151-2160

  • DOI: https://doi.org/10.1016/j.str.2012.09.019
  • Primary Citation of Related Structures:  
    4FTX, 4FUW

  • PubMed Abstract: 

    The yeast EGO complex, consisting of Gtr1, Gtr2, Ego1, and Ego3, localizes to the endosomal and vacuolar membranes and plays a pivotal role in cell growth and autophagy regulation through relaying amino acid signals to activate TORC1. Here, we report the crystal structures of a wild-type and a mutant form of Saccharomyces cerevisiae Ego3. Ego3 assumes a homodimeric structure similar to that of the mammalian MP1-p14 heterodimer and the C-terminal domains of the yeast Gtr1-Gtr2 heterodimer, both of which function in TORC1 signaling. Structural and genetic data demonstrate that the unique dimer conformation of Ego3 is essential for the integrity and function of the EGO complex. Structural and functional data also identify a potential binding site for Gtr1-Gtr2. These results suggest a structural conservation of the protein components involved in amino acid signaling to TORC1 and reveal structural insights into the molecular mechanism of Ego3 function in TORC1 signaling.


  • Organizational Affiliation

    State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological 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
Protein SLM4
A, B
170Saccharomyces 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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SIN
Query on SIN

Download Ideal Coordinates CCD File 
C [auth B]SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.959α = 90
b = 99.311β = 90
c = 159.106γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-28
    Type: Initial release
  • Version 1.1: 2013-09-04
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations