6S6D

Crystal structure of RagA-Q66L-GTP/RagC-S75N-GDP GTPase heterodimer complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.213 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Architecture of human Rag GTPase heterodimers and their complex with mTORC1.

Anandapadamanaban, M.Masson, G.R.Perisic, O.Berndt, A.Kaufman, J.Johnson, C.M.Santhanam, B.Rogala, K.B.Sabatini, D.M.Williams, R.L.

(2019) Science 366: 203-210

  • DOI: https://doi.org/10.1126/science.aax3939
  • Primary Citation of Related Structures:  
    6S6A, 6S6D, 6SB0, 6SB2

  • PubMed Abstract: 

    The Rag guanosine triphosphatases (GTPases) recruit the master kinase mTORC1 to lysosomes to regulate cell growth and proliferation in response to amino acid availability. The nucleotide state of Rag heterodimers is critical for their association with mTORC1. Our cryo-electron microscopy structure of RagA/RagC in complex with mTORC1 shows the details of RagA/RagC binding to the RAPTOR subunit of mTORC1 and explains why only the RagA GTP /RagC GDP nucleotide state binds mTORC1. Previous kinetic studies suggested that GTP binding to one Rag locks the heterodimer to prevent GTP binding to the other. Our crystal structures and dynamics of RagA/RagC show the mechanism for this locking and explain how oncogenic hotspot mutations disrupt this process. In contrast to allosteric activation by RHEB, Rag heterodimer binding does not change mTORC1 conformation and activates mTORC1 by targeting it to lysosomes.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related GTP-binding protein AA,
C [auth B]
313Homo sapiensMutation(s): 1 
Gene Names: RRAGA
EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q7L523 (Homo sapiens)
Explore Q7L523 
Go to UniProtKB:  Q7L523
PHAROS:  Q7L523
GTEx:  ENSG00000155876 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7L523
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related GTP-binding protein CB [auth C],
D
399Homo sapiensMutation(s): 1 
Gene Names: RRAGC
EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HB90 (Homo sapiens)
Explore Q9HB90 
Go to UniProtKB:  Q9HB90
PHAROS:  Q9HB90
GTEx:  ENSG00000116954 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HB90
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
G [auth C],
L [auth D]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
9JE
Query on 9JE

Download Ideal Coordinates CCD File 
J [auth B],
K [auth B]
pentane-1,5-diol
C5 H12 O2
ALQSHHUCVQOPAS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.504α = 90
b = 81.439β = 90
c = 246.033γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_U105184308
Cancer Research UKUnited KingdomC14801/A21211

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-16
    Type: Initial release
  • Version 1.1: 2019-10-23
    Changes: Data collection, Database references
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references, Derived calculations