3R7W

Crystal Structure of Gtr1p-Gtr2p complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 
    0.283 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.236 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.238 (Depositor) 

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Ligand Structure Quality Assessment 

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Literature

Crystal structure of the Gtr1p-Gtr2p complex reveals new insights into the amino acid-induced TORC1 activation

Gong, R.Li, L.Liu, Y.Wang, P.Yang, H.Wang, L.Cheng, J.Guan, K.L.Xu, Y.

(2011) Genes Dev 25: 1668-1673

  • DOI: https://doi.org/10.1101/gad.16968011
  • Primary Citation of Related Structures:  
    3R7W

  • PubMed Abstract: 

    The target of rapamycin (TOR) complex 1 (TORC1) is a central cell growth regulator in response to a wide array of signals. The Rag GTPases play an essential role in relaying amino acid signals to TORC1 activation through direct interaction with raptor and recruitment of the TORC1 complex to lysosomes. Here we present the crystal structure of the Gtr1p-Gtr2p complex, the Rag homologs from Saccharomyces cerevisiae, at 2.8 Å resolution. The heterodimeric GTPases reveal a pseudo-twofold symmetric organization. Structure-guided functional analyses of RagA-RagC, the human homologs of Gtr1p-Gtr2p, show that both G domains (N-terminal GTPase domains) and dimerization are important for raptor binding. In particular, the switch regions of the G domain in RagA are indispensible for interaction with raptor, and hence TORC1 activation. The dimerized C-terminal domains of RagA-RagC display a remarkable structural similarity to MP1/p14, which is in a complex with lysosome membrane protein p18, and directly interact with p18, therefore recruiting mTORC1 to the lysosome for activation by Rheb. Our results reveal a structural model for the mechanism of the Rag GTPases in TORC1 activation and amino acid signaling.


  • Organizational Affiliation

    Cancer Institute, Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding protein GTR1
A, C
307Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: GTR1
EC: 3.6.5
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
3R7W_1
020406080100120140160180200220240260280300
3R7W_1
UNIPROT Q00582
UNMODELED
ARTIFACT
MODIFIED MONOMER
HYDROPATHY
DISORDER
DISORDERED BINDING
PFAM
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding protein GTR2
B, D
331Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: GTR2
EC: 3.6.5
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
3R7W_2
050100150200250300
3R7W_2
UNIPROT P53290
UNMODELED
MODIFIED MONOMER
HYDROPATHY
DISORDER
DISORDERED BINDING
PFAM
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free:  0.283 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.236 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.238 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.908α = 90
b = 148.439β = 100.61
c = 98.508γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SOLVEphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GNPClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-24
    Type: Initial release
  • Version 1.1: 2013-06-19
    Changes: Database references
  • Version 1.2: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary