Wildtype rat TRPV2 in nanodiscs bound to RR and 2-APB

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

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Molecular details of ruthenium red pore block in TRPV channels.

Pumroy, R.A.De Jesus-Perez, J.J.Protopopova, A.D.Rocereta, J.A.Fluck, E.C.Fricke, T.Lee, B.H.Rohacs, T.Leffler, A.Moiseenkova-Bell, V.

(2024) EMBO Rep 25: 506-523

  • DOI: https://doi.org/10.1038/s44319-023-00050-0
  • Primary Citation of Related Structures:  
    8FFL, 8FFM, 8FFN, 8FFQ

  • PubMed Abstract: 

    Transient receptor potential vanilloid (TRPV) channels play a critical role in calcium homeostasis, pain sensation, immunological response, and cancer progression. TRPV channels are blocked by ruthenium red (RR), a universal pore blocker for a wide array of cation channels. Here we use cryo-electron microscopy to reveal the molecular details of RR block in TRPV2 and TRPV5, members of the two TRPV subfamilies. In TRPV2 activated by 2-aminoethoxydiphenyl borate, RR is tightly coordinated in the open selectivity filter, blocking ion flow and preventing channel inactivation. In TRPV5 activated by phosphatidylinositol 4,5-bisphosphate, RR blocks the selectivity filter and closes the lower gate through an interaction with polar residues in the pore vestibule. Together, our results provide a detailed understanding of TRPV subfamily pore block, the dynamic nature of the selectivity filter and allosteric communication between the selectivity filter and lower gate.

  • Organizational Affiliation

    Institute for Neurophysiology, Hannover Medical School, 30625, Hannover, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transient receptor potential cation channel subfamily V member 2
A, B, C, D
761Rattus norvegicusMutation(s): 0 
Gene Names: Trpv2Sac2bVrl1
Find proteins for Q9WUD2 (Rattus norvegicus)
Explore Q9WUD2 
Go to UniProtKB:  Q9WUD2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WUD2
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
R2R (Subject of Investigation/LOI)
Query on R2R

Download Ideal Coordinates CCD File 
G [auth A]ruthenium(6+) azanide pentaamino(oxido)ruthenium (1/4/2)
H28 N14 O2 Ru3
Query on PEX

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
J [auth C],
L [auth D]
C25 H49 N O8 P
Query on FZ4

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
K [auth C],
M [auth D]
2-aminoethyl diphenylborinate
C14 H16 B N O
Experimental Data & Validation

Experimental Data

  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM144120

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-07
    Type: Initial release
  • Version 1.1: 2024-02-21
    Changes: Database references