6C08

Zebrafish SLC38A9 with arginine bound in the cytosol open state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.17 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.267 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of arginine-bound lysosomal transporter SLC38A9 in the cytosol-open state.

Lei, H.T.Ma, J.Sanchez Martinez, S.Gonen, T.

(2018) Nat. Struct. Mol. Biol. 25: 522-527

  • DOI: 10.1038/s41594-018-0072-2

  • PubMed Abstract: 
  • Recent advances in understanding intracellular amino acid transport and mechanistic target of rapamycin complex 1 (mTORC1) signaling shed light on solute carrier 38, family A member 9 (SLC38A9), a lysosomal transporter responsible for the binding and ...

    Recent advances in understanding intracellular amino acid transport and mechanistic target of rapamycin complex 1 (mTORC1) signaling shed light on solute carrier 38, family A member 9 (SLC38A9), a lysosomal transporter responsible for the binding and translocation of several essential amino acids. Here we present the first crystal structure of SLC38A9 from Danio rerio in complex with arginine. As captured in the cytosol-open state, the bound arginine was locked in a transitional state stabilized by transmembrane helix 1 (TM1) of drSLC38A9, which was anchored at the groove between TM5 and TM7. These anchoring interactions were mediated by the highly conserved WNTMM motif in TM1, and mutations in this motif abolished arginine transport by drSLC38A9. The underlying mechanism of substrate binding is critical for sensitizing the mTORC1 signaling pathway to amino acids and for maintenance of lysosomal amino acid homeostasis. This study offers a first glimpse into a prototypical model for SLC38 transporters.


    Organizational Affiliation

    Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
antibody Fab Heavy Chain
A, D
218N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
antibody Fab light chain
B, E
215N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Sodium-coupled neutral amino acid transporter 9
C, F
479Danio rerioMutation(s): 4 
Gene Names: slc38a9
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Solute Carrier (SLC) Transporter Superfamily
Protein: 
SLC38A9 lysosomal amino acid transporter, cytosol-open state
Find proteins for Q08BA4 (Danio rerio)
Go to UniProtKB:  Q08BA4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ARG
Query on ARG

Download SDF File 
Download CCD File 
F
ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
A, D
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.17 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.267 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 136.613α = 90.00
b = 82.808β = 100.02
c = 158.922γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-12-28 
  • Released Date: 2018-06-20 
  • Deposition Author(s): Lei, H.-T., Gonen, T.

Revision History 

  • Version 1.0: 2018-06-20
    Type: Initial release