9ISG | pdb_00009isg

Structure of rat TRPV1 in complex with PSFL426-S5

• PDB DOI: https://doi.org/10.2210/pdb9ISG/pdb
• EM Map EMD-60835: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-07-17 Released: 2025-07-23 
• Deposition Author(s): Chen, X., Yu, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mechanism of capsaicin entry into buried vanilloid sites in TRPV1.

Sun, M.Y., Bian, Y.J., Chen, X.Y., Zhang, X., Li, M., Zhou, B.Y., Yang, Y., Huang, Y.Z., Yang, R., Gao, Y.H., Cui, W.W., Wang, Y.Q., Zhu, S.J., Cao, P., Li, C.Z., Zhu, M.X., Lei, Y.T., Yang, F., Yu, Y.

(2025) Nat Chem Biol 21: 1957-1969

• PubMed: 40702302 
• DOI: https://doi.org/10.1038/s41589-025-01966-5
• Primary Citation of Related Structures:  
  9ISG


• PubMed Abstract: 
  

  The transient receptor potential vanilloid 1 (TRPV1) receptor is a promising target for nonopioid analgesics, yet hyperthermic side effects have hindered drug development. The prevailing perspective maintains that extracellular hydrophobic vanilloid ligands, such as capsaicin, traverse the cell membrane to reach the buried vanilloid site during TRPV1 activation. Here, we present an alternative mechanism based on computational and experimental approaches, which suggests a distinct hydrophobic pathway at the TRPV1-cell membrane interface as the principal route for ligand entry to the vanilloid site, rather than direct membrane penetration. Modifications to residues within this pathway greatly delayed capsaicin entry without directly modulating TRPV1 channel gating. A compound designed to occupy this pathway's entrance exhibited analgesic effects without inducing hyperthermia. Cryo-electron microscopy confirmed binding to TRPV1 and its role in perturbing capsaicin entry. Thus, our findings unveil a unique and targetable route for capsaicin access to the TRPV1 vanilloid site.

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Organizational Affiliation: 
• Schools of Basic Medicine and Clinical Pharmacy, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.
Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China.
Department of Biophysics and Kidney Disease Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
Liang zhu Laboratory, Zhejiang University Medical Center, Hangzhou, China.
Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China.
Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China.
Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA.
Schools of Basic Medicine and Clinical Pharmacy, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China. [e-mail].
Department of Biophysics and Kidney Disease Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China. [e-mail].
Liang zhu Laboratory, Zhejiang University Medical Center, Hangzhou, China. [e-mail].
Schools of Basic Medicine and Clinical Pharmacy, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China. [e-mail].
Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China. [e-mail].
Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 399.22 kDa 
• Atom Count: 17,220 
• Modeled Residue Count: 2,112 
• Deposited Residue Count: 3,516 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transient receptor potential cation channel subfamily V member 1	A, B, C, D	879	Rattus norvegicus	Mutation(s): 0  Gene Names: Trpv1, Vr1, Vr1l
UniProt
Find proteins for O35433 (Rattus norvegicus) Explore O35433  Go to UniProtKB:  O35433

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1D92	E [auth A], F [auth B], G [auth C], H [auth D]	4-azanyl-3-sulfanylidene-1,2,4-triazine-5,6-dione C3 H2 N4 O2 S XSWNQPGETDYNIH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-23 
Deposition Author(s): Chen, X., Yu, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32371289

Revision History  

• Version 1.0: 2025-07-23
  Type: Initial release
  
• Version 1.1: 2025-08-13
  Changes: Data collection, Database references
• Version 1.2: 2025-12-10
  Changes: Data collection, Database references