7ZJH | pdb_00007zjh

TRPV2-C16+Pro-2

• PDB DOI: https://doi.org/10.2210/pdb7ZJH/pdb
• EM Map EMD-14748: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2022-04-11 Released: 2023-01-18 
• Deposition Author(s): Zhang, L., Gourdon, P., Zygmunt, P.M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.39 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cannabinoid non-cannabidiol site modulation of TRPV2 structure and function.

Zhang, L., Simonsen, C., Zimova, L., Wang, K., Moparthi, L., Gaudet, R., Ekoff, M., Nilsson, G., Hellmich, U.A., Vlachova, V., Gourdon, P., Zygmunt, P.M.

(2022) Nat Commun 13: 7483-7483

• PubMed: 36470868 
• DOI: https://doi.org/10.1038/s41467-022-35163-y
• Primary Citation Related Structures: 
  7ZJD, 7ZJE, 7ZJG, 7ZJH, 7ZJI


• PubMed Abstract: 
  

  TRPV2 is a ligand-operated temperature sensor with poorly defined pharmacology. Here, we combine calcium imaging and patch-clamp electrophysiology with cryo-electron microscopy (cryo-EM) to explore how TRPV2 activity is modulated by the phytocannabinoid Δ ⁹ -tetrahydrocannabiorcol (C16) and by probenecid. C16 and probenecid act in concert to stimulate TRPV2 responses including histamine release from rat and human mast cells. Each ligand causes distinct conformational changes in TRPV2 as revealed by cryo-EM. Although the binding for probenecid remains elusive, C16 associates within the vanilloid pocket. As such, the C16 binding location is distinct from that of cannabidiol, partially overlapping with the binding site of the TRPV2 inhibitor piperlongumine. Taken together, we discover a new cannabinoid binding site in TRPV2 that is under the influence of allosteric control by probenecid. This molecular insight into ligand modulation enhances our understanding of TRPV2 in normal and pathophysiology.

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Organizational Affiliation: 
• Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden.
Department of Experimental Medical Science, Lund University, Lund, Sweden.
Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark.
Department of Cellular Neurophysiology, Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic.
Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden.
Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.
Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
Division Immunology and Allergy Unit, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Solna, Sweden.
Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry and Cluster of Excellence "Balance of the Microverse", Friedrich Schiller University Jena, Jena, Germany.
Center for Biomolecular Magnetic Resonance, Goethe-University, Frankfurt/Main, Germany.
Department of Experimental Medical Science, Lund University, Lund, Sweden. [e-mail].
Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark. [e-mail].
Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 465.71 kDa 
• Atom Count: 18,984 
• Modeled Residue Count: 2,344 
• Deposited Residue Count: 4,104 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transient receptor potential cation channel subfamily V member 2	A, B [auth D], C, D [auth B]	1,026	Rattus norvegicus	Mutation(s): 0  Gene Names: Trpv2 Membrane Entity: Yes
UniProt
Find proteins for Q9WUD2 (Rattus norvegicus) Explore Q9WUD2  Go to UniProtKB:  Q9WUD2

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.39 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-01-18 
Deposition Author(s): Zhang, L., Gourdon, P., Zygmunt, P.M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-01-18
  Type: Initial release
  
• Version 1.1: 2024-07-24
  Changes: Data collection
• Version 1.2: 2025-07-02
  Changes: Data collection, Structure summary