9IRC | pdb_00009irc

CyroEM structure of hSLC15A4+TASL+Fab235

• PDB DOI: https://doi.org/10.2210/pdb9IRC/pdb
• EM Map EMD-60809: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Spodoptera frugiperda, Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  MemProtMD


• Deposited: 2024-07-15 Released: 2025-08-20 
• Deposition Author(s): Zhu, Y.L., Zhang, Q.X., Gao, P.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.82 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Development of conformation-selective antibodies targeting human SLC15A4.

Zhu, Y., Zhang, X., Zhang, Q., Sun, P., Liu, K., Nie, X., Ma, J., Zhang, L., Gao, Y., Wang, Y., Liu, S., Gao, A., Zhang, L., Gao, P.

(2025) Nat Commun 16: 7324-7324

• PubMed: 40781080 
• DOI: https://doi.org/10.1038/s41467-025-62759-x
• Primary Citation Related Structures: 
  9IRB, 9IRC


• PubMed Abstract: 
  

  SLC15A4, an endolysosomal solute carrier family transporter, plays a critical role in TLR7/8/9-induced immune responses through assembling a complex with the downstream adaptor TASL in a conformation-dependent manner. Despite its close functional association and promising therapeutic potential in infections, tumors, and autoimmune diseases, the development of conformation-specific antibodies for human SLC15A4 (hSLC15A4) remains challenging. Here, using a systematic screening and validation approach, we identify a pair of conformation-selective antibodies, clones 107 and 235, targeting the endolysosomal lumen surface of hSLC15A4 with opposite conformation-regulatory activities. Specifically, clone 107 selectively binds to hSLC15A4 in a TASL binding-incompetent luminal-open state; whereas clone 235 stabilizes hSLC15A4 in a TASL binding-competent cytoplasmic-open state. Our research identifies antibodies that recognize distinct conformations of hSLC15A4, potentially enabling modulation of the TLR7/8/9 pathway and contributing to the development of targeted therapies and research tools selectively targeting hSLC15A4.

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Organizational Affiliation: 
• Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing, China.
State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
University of Chinese Academy of Sciences, Beijing, China.
Department of Nutrition and Health, Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, China.
Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing, China. [e-mail].
Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China. [e-mail].
State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, China. [e-mail].
State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, China. [e-mail].
Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 109.19 kDa 
• Atom Count: 5,589 
• Modeled Residue Count: 726 
• Deposited Residue Count: 1,000 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Solute carrier family 15 member 4	A	602	Homo sapiens	Mutation(s): 0  Gene Names: SLC15A4, PHT1, PTR4, FP12591 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N697 (Homo sapiens) Explore Q8N697  Go to UniProtKB:  Q8N697
PHAROS:  Q8N697 GTEx:  ENSG00000139370

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TLR adapter interacting with SLC15A4 on the lysosome	B	170	Mus musculus	Mutation(s): 0  Gene Names: Tasl Membrane Entity: Yes
UniProt
Find proteins for Q9D3J9 (Mus musculus) Explore Q9D3J9  Go to UniProtKB:  Q9D3J9

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab235 heavy chain	C [auth H]	120	Mus musculus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab235 light chain	D [auth L]	108	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.82 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-08-20 
Deposition Author(s): Zhu, Y.L., Zhang, Q.X., Gao, P.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32200989

Revision History  

• Version 1.0: 2025-08-20
  Type: Initial release