7KGV

Crystal structure of sodium-coupled neutral amino acid transporter SLC38A9 in the N-terminal plugged form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.252 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A conformational change in the N terminus of SLC38A9 signals mTORC1 activation.

Lei, H.T.Mu, X.Hattne, J.Gonen, T.

(2021) Structure 29: 426

  • DOI: https://doi.org/10.1016/j.str.2020.11.014
  • Primary Citation of Related Structures:  
    7KGV

  • PubMed Abstract: 

    mTORC1 is a central hub that integrates environmental cues, such as cellular stresses and nutrient availability to modulate metabolism and cellular responses. Recently, SLC38A9, a lysosomal amino acid transporter, emerged as a sensor for luminal arginine and as an activator of mTORC1. The amino acid-mediated activation of mTORC1 is regulated by the N-terminal domain of SLC38A9. Here, we determined the crystal structure of zebrafish SLC38A9 (drSLC38A9) and found the N-terminal fragment inserted deep within the transporter, bound in the substrate-binding pocket where normally arginine would bind. This represents a significant conformational change of the N-terminal domain (N-plug) when compared with our recent arginine-bound structure of drSLC38A9. We propose a ball-and-chain model for mTORC1 activation, where N-plug insertion and Rag GTPase binding with SLC38A9 is regulated by luminal arginine levels. This work provides important insights into nutrient sensing by SLC38A9 to activate the mTORC1 pathways in response to dietary amino acids.


  • Organizational Affiliation

    Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium-coupled neutral amino acid transporter 9
A, B
549Danio rerioMutation(s): 4 
Gene Names: slc38a9zgc:154088
Membrane Entity: Yes 
UniProt
Find proteins for Q08BA4 (Danio rerio)
Explore Q08BA4 
Go to UniProtKB:  Q08BA4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08BA4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Monoclonal antibody Fab heavy chain
C, D
219Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Monoclonal antibody Fab light chain
E, F
215Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.252 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.798α = 90
b = 82.514β = 106.024
c = 158.59γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
Cootmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-23
    Type: Initial release
  • Version 1.1: 2021-05-19
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description