6PVL | pdb_00006pvl

Cryo-EM structure of mouse TRPV3 in closed state at 42 degrees Celsius

• PDB DOI: https://doi.org/10.2210/pdb6PVL/pdb
• EM Map EMD-20492: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2019-07-21 Released: 2019-10-23 
• Deposition Author(s): Singh, A.K., McGoldrick, L.L., Sobolevsky, A.I.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of temperature sensation by the TRP channel TRPV3.

Singh, A.K., McGoldrick, L.L., Demirkhanyan, L., Leslie, M., Zakharian, E., Sobolevsky, A.I.

(2019) Nat Struct Mol Biol 26: 994-998

• PubMed: 31636415 
• DOI: https://doi.org/10.1038/s41594-019-0318-7
• Primary Citation Related Structures: 
  6PVL, 6PVM, 6PVN, 6PVO, 6PVP, 6PVQ


• PubMed Abstract: 
  

  We present structures of mouse TRPV3 in temperature-dependent open, closed and intermediate states that suggest two-step activation of TRPV3 by heat. During the strongly temperature-dependent first step, sensitization, the channel pore remains closed while S6 helices undergo α-to-π transitions. During the weakly temperature-dependent second step, channel opening, tight association of the S1-S4 and pore domains is stabilized by changes in the carboxy-terminal and linker domains.

---

Organizational Affiliation: 
• Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY, USA.
Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine, Peoria, IL, USA.
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA. [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: gel filtration

Macromolecule Content 

• Total Structure Weight: 370.57 kDa 
• Atom Count: 21,006 
• Modeled Residue Count: 2,576 
• Deposited Residue Count: 3,232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transient receptor potential cation channel subfamily V member 3	A, B, C, D	808	Mus musculus	Mutation(s): 0  Gene Names: Trpv3 Membrane Entity: Yes
UniProt
Find proteins for Q8K424 (Mus musculus) Explore Q8K424  Go to UniProtKB:  Q8K424

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA (Subject of Investigation/LOI)	E [auth A], F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-10-23 
Deposition Author(s): Singh, A.K., McGoldrick, L.L., Sobolevsky, A.I.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01 CA206573

Revision History  

• Version 1.0: 2019-10-23
  Type: Initial release
  
• Version 1.1: 2019-11-06
  Changes: Data collection, Database references
• Version 1.2: 2019-11-27
  Changes: Database references
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence
• Version 1.4: 2024-03-20
  Changes: Data collection, Database references