RR-bound wildtype rabbit TRPV5 in nanodiscs

Experimental Data Snapshot

  • Resolution: 2.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


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 5
A, B, C, D
739Oryctolagus cuniculusMutation(s): 0 
Gene Names: Trpv5Ecac1
Membrane Entity: Yes 
Find proteins for Q9XSM3 (Oryctolagus cuniculus)
Explore Q9XSM3 
Go to UniProtKB:  Q9XSM3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XSM3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on POV

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
J [auth B]
K [auth B]
N [auth C]
F [auth A],
G [auth A],
J [auth B],
K [auth B],
N [auth C],
O [auth C],
R [auth D],
S [auth D]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
R2R (Subject of Investigation/LOI)
Query on R2R

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

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
L [auth B]
M [auth B]
P [auth C]
H [auth A],
I [auth A],
L [auth B],
M [auth B],
P [auth C],
Q [auth C],
T [auth D],
U [auth D]
C28 H44 O
Experimental Data & Validation

Experimental Data

  • Resolution: 2.96 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