8WX2 | pdb_00008wx2

Cryo-EM structure of human SLC15A3 (dimer)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.44 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8WX2

This is version 1.5 of the entry. See complete history

Literature

The structures of the peptide transporters SLC15A3 and SLC15A4 reveal the recognition mechanisms for substrate and TASL.

Zhang, Z.Kasai, S.Sakaniwa, K.Fujimura, A.Ohto, U.Shimizu, T.

(2025) Structure 33: 330

  • DOI: https://doi.org/10.1016/j.str.2024.11.019
  • Primary Citation Related Structures: 
    8WX1, 8WX2, 8WX3, 8WX4, 8WX5

  • PubMed Abstract: 

    The solute carrier family 15 members 3 and 4 (SLC15A3 and SLC15A4) are closely related endolysosomal peptide transporters that transport free histidine and certain dipeptides from the lumen to cytosol. Besides, SLC15A4 also functions as a scaffold protein for the recruitment of the adapter TASL for interferon regulatory factor 5 (IRF5) activation downstream of innate immune TLR7-9 signaling. However, the molecular basis for the substrate recognition and TASL recruitment by these membrane proteins is not well understood. Here, we report the cryoelectron microscopy (cryo-EM) structure of apo SLC15A3 and structures of SLC15A4 in the absence or presence of the substrate, revealing the specific dipeptide recognition mechanism. Each SLC15A3 and SLC15A4 protomer adopts an outward-facing conformation. Furthermore, we also present the cryo-EM structure of a SLC15A4-TASL complex. The N terminal region of TASL forms a helical structure that inserts deeply into the inward-facing cavity of SLC15A4.


  • Organizational Affiliation
    • Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

Macromolecule Content 

  • Total Structure Weight: 134.28 kDa 
  • Atom Count: 6,800 
  • Modeled Residue Count: 880 
  • Deposited Residue Count: 1,218 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Solute carrier family 15 member 3
A, B
609Homo sapiensMutation(s): 0 
Gene Names: SLC15A3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IY34 (Homo sapiens)
Explore Q8IY34 
Go to UniProtKB:  Q8IY34
PHAROS:  Q8IY34
GTEx:  ENSG00000110446 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IY34
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.44 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-06
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Structure summary
  • Version 1.2: 2024-10-16
    Changes: Data collection, Structure summary
  • Version 1.3: 2025-06-18
    Changes: Data collection, Database references
  • Version 1.4: 2025-06-25
    Changes: Data collection, Database references
  • Version 1.5: 2025-07-02
    Changes: Data collection