6C08 | pdb_00006c08

Zebrafish SLC38A9 with arginine bound in the cytosol open state

• PDB DOI: https://doi.org/10.2210/pdb6C08/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Mus musculus, Danio rerio
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.17 Å
• R-Value Free: 
  0.285 (Depositor), 0.297 (DCC) 
• R-Value Work: 
  0.267 (Depositor), 0.275 (DCC) 
• R-Value Observed: 
  0.267 (Depositor) 

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

• PubMed: 29872228 
• DOI: https://doi.org/10.1038/s41594-018-0072-2
• Primary Citation Related Structures: 
  6C08


• 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 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.

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Organizational Affiliation: 
• Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, USA.
Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA. [e-mail].
Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, USA. [e-mail].
Departments of Physiology and Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 200.62 kDa 
• Atom Count: 12,341 
• Modeled Residue Count: 1,607 
• Deposited Residue Count: 1,824 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody Fab Heavy Chain	A, D	218	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody Fab light chain	B, E	215	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium-coupled neutral amino acid transporter 9	C, F	479	Danio rerio	Mutation(s): 4  Gene Names: slc38a9, zgc:154088 Membrane Entity: Yes
UniProt
Find proteins for Q08BA4 (Danio rerio) Explore Q08BA4  Go to UniProtKB:  Q08BA4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ARG	G [auth F]	ARGININE C6 H15 N4 O2 ODKSFYDXXFIFQN-BYPYZUCNSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.17 Å
• R-Value Free:  0.285 (Depositor), 0.297 (DCC) 
• R-Value Work:  0.267 (Depositor), 0.275 (DCC) 
• R-Value Observed: 0.267 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.613	α = 90
b = 82.808	β = 100.02
c = 158.922	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2018-06-20
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Structure summary