6SB2

cryo-EM structure of mTORC1 bound to active RagA/C GTPases


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1126/science.aax3939
  • Structures With Same Primary Citation

  • 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 wit ...

    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. rlw@mrc-lmb.cam.ac.uk.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
mTOR,Serine/threonine-protein kinase mTOR,mTOR,Serine/threonine-protein kinase mTOR
A, B
2549Homo sapiensMutation(s): 0 
Gene Names: MTOR
EC: 2.7.11.1
Find proteins for P42345 (Homo sapiens)
Go to UniProtKB:  P42345
NIH Common Fund Data Resources
PHAROS  P42345

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Target of rapamycin complex subunit LST8
E, H
326Homo sapiensMutation(s): 0 
Gene Names: MLST8GBLLST8
Find proteins for Q9BVC4 (Homo sapiens)
Go to UniProtKB:  Q9BVC4
NIH Common Fund Data Resources
PHAROS  Q9BVC4

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ras-related GTP-binding protein A
C, I
313Homo sapiensMutation(s): 1 
Gene Names: RRAGA
Find proteins for Q7L523 (Homo sapiens)
Go to UniProtKB:  Q7L523
NIH Common Fund Data Resources
PHAROS  Q7L523

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Ras-related GTP-binding protein C
D, J
399Homo sapiensMutation(s): 1 
Gene Names: RRAGC
Find proteins for Q9HB90 (Homo sapiens)
Go to UniProtKB:  Q9HB90
NIH Common Fund Data Resources
PHAROS  Q9HB90

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Regulatory-associated protein of mTOR
N, Y
1335Homo sapiensMutation(s): 0 
Gene Names: RPTORKIAA1303RAPTOR
Find proteins for Q8N122 (Homo sapiens)
Go to UniProtKB:  Q8N122
NIH Common Fund Data Resources
PHAROS  Q8N122
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download CCD File 
C, I
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
GDP
Query on GDP

Download CCD File 
D, J
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_U105184308
Cancer Research UKUnited KingdomC14801/A21211
European Molecular Biology OrganizationUnited Kingdomlong-term fellowship

Revision History 

  • Version 1.0: 2019-10-16
    Type: Initial release
  • Version 1.1: 2019-10-23
    Changes: Data collection, Database references