6WJ2

CryoEM structure of the SLC38A9-RagA-RagC-Ragulator complex in the pre-GAP state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural mechanism for amino acid-dependent Rag GTPase nucleotide state switching by SLC38A9.

Fromm, S.A.Lawrence, R.E.Hurley, J.H.

(2020) Nat Struct Mol Biol 27: 1017-1023

  • DOI: https://doi.org/10.1038/s41594-020-0490-9
  • Primary Citation of Related Structures:  
    6WJ2, 6WJ3

  • PubMed Abstract: 

    The Rag GTPases (Rags) recruit mTORC1 to the lysosomal membrane in response to nutrients, where it is then activated in response to energy and growth factor availability. The lysosomal folliculin (FLCN) complex (LFC) consists of the inactive Rag dimer, the pentameric scaffold Ragulator, and the FLCN:FNIP2 (FLCN-interacting protein 2) GTPase activating protein (GAP) complex, and prevents Rag dimer activation during amino acid starvation. How the LFC is disassembled upon amino acid refeeding is an outstanding question. Here we show that the cytoplasmic tail of the human lysosomal solute carrier family 38 member 9 (SLC38A9) destabilizes the LFC and thereby triggers GAP activity of FLCN:FNIP2 toward RagC. We present the cryo-EM structures of Rags in complex with their lysosomal anchor complex Ragulator and the cytoplasmic tail of SLC38A9 in the pre- and post-GTP hydrolysis state of RagC, which explain how SLC38A9 destabilizes the LFC and so promotes Rag dimer activation.


  • Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR1166Homo sapiensMutation(s): 1 
Gene Names: LAMTOR1C11orf59PDROPP7157
UniProt & NIH Common Fund Data Resources
Find proteins for Q6IAA8 (Homo sapiens)
Explore Q6IAA8 
Go to UniProtKB:  Q6IAA8
PHAROS:  Q6IAA8
GTEx:  ENSG00000149357 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6IAA8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR2127Homo sapiensMutation(s): 0 
Gene Names: LAMTOR2MAPBPIPROBLD3HSPC003
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2Q5 (Homo sapiens)
Explore Q9Y2Q5 
Go to UniProtKB:  Q9Y2Q5
PHAROS:  Q9Y2Q5
GTEx:  ENSG00000116586 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y2Q5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR3124Homo sapiensMutation(s): 0 
Gene Names: LAMTOR3MAP2K1IP1MAPKSP1PRO2783
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHA4 (Homo sapiens)
Explore Q9UHA4 
Go to UniProtKB:  Q9UHA4
PHAROS:  Q9UHA4
GTEx:  ENSG00000109270 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UHA4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR499Homo sapiensMutation(s): 0 
Gene Names: LAMTOR4C7orf59
UniProt & NIH Common Fund Data Resources
Find proteins for Q0VGL1 (Homo sapiens)
Explore Q0VGL1 
Go to UniProtKB:  Q0VGL1
PHAROS:  Q0VGL1
GTEx:  ENSG00000188186 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0VGL1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR5173Homo sapiensMutation(s): 0 
Gene Names: LAMTOR5HBXIPhCG_40252
UniProt & NIH Common Fund Data Resources
Find proteins for O43504 (Homo sapiens)
Explore O43504 
Go to UniProtKB:  O43504
PHAROS:  O43504
GTEx:  ENSG00000134248 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43504
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related GTP-binding protein A336Homo sapiensMutation(s): 0 
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: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related GTP-binding protein C404Homo 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium-coupled neutral amino acid transporter 9122Homo sapiensMutation(s): 0 
Gene Names: SLC38A9URLC11
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NBW4 (Homo sapiens)
Explore Q8NBW4 
Go to UniProtKB:  Q8NBW4
PHAROS:  Q8NBW4
GTEx:  ENSG00000177058 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NBW4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L8S
Query on L8S

Download Ideal Coordinates CCD File 
J [auth G]9-{5-O-[(S)-hydroxy{[(R)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]-alpha-L-arabinofuranosyl}-3,9-dihydro-1H-purine-2,6-dione
C10 H15 N4 O14 P3 S
IAOZVDCRMYYKMQ-BZKDHIKHSA-N
GDP
Query on GDP

Download Ideal Coordinates CCD File 
I [auth F]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
K [auth G]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM111730

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-02
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Database references
  • Version 1.2: 2020-11-18
    Changes: Database references
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references, Refinement description