8TF2 | pdb_00008tf2

Wildtype rabbit TRPV5 into nanodiscs in Apo state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8TF2

This is version 1.1 of the entry. See complete history

Literature

Structural mechanism of TRPV5 inhibition by econazole.

De Jesus-Perez, J.J.Gabrielle, M.Raheem, S.Fluck, E.C.Rohacs, T.Moiseenkova-Bell, V.Y.

(2024) Structure 32: 148-156.e5

  • DOI: https://doi.org/10.1016/j.str.2023.11.012
  • Primary Citation Related Structures: 
    8TF2, 8TF3, 8TF4

  • PubMed Abstract: 

    The calcium-selective TRPV5 channel activated by phosphatidylinositol 4,5-bisphosphate [PI(4,5)P 2 ] is involved in calcium homeostasis. Recently, cryoelectron microscopy (cryo-EM) provided molecular details of TRPV5 modulation by exogenous and endogenous molecules. However, the details of TRPV5 inhibition by the antifungal agent econazole (ECN) remain elusive due to the low resolution of the currently available structure. In this study, we employ cryo-EM to comprehensively examine how the ECN inhibits TRPV5. By combining our structural findings with site-directed mutagenesis, calcium measurements, electrophysiology, and molecular dynamics simulations, we determined that residues F472 and L475 on the S4 helix, along with residue W495 on the S5 helix, collectively constitute the ECN-binding site. Additionally, the structure of TRPV5 in the presence of ECN and PI(4,5)P 2 , which does not show the bound activator, reveals a potential inhibition mechanism in which ECN competes with PI(4,5)P 2 , preventing the latter from binding, and ultimately pore closure.


  • Organizational Affiliation
    • Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

Macromolecule Content 

  • Total Structure Weight: 350.44 kDa 
  • Atom Count: 19,856 
  • Modeled Residue Count: 2,408 
  • Deposited Residue Count: 2,956 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 
UniProt
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
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CPL
(Subject of Investigation/LOI)

Query on CPL



Download:Ideal Coordinates CCD File
BA [auth D]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
BA [auth D],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth B],
P [auth B],
Q [auth B],
R [auth C],
U [auth C],
V [auth C],
W [auth C],
X [auth C],
Y [auth D]
1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C42 H80 N O8 P
JLPULHDHAOZNQI-ZTIMHPMXSA-N
ERG

Query on ERG



Download:Ideal Coordinates CCD File
AA [auth D]
E [auth A]
F [auth A]
N [auth B]
O [auth B]
AA [auth D],
E [auth A],
F [auth A],
N [auth B],
O [auth B],
S [auth C],
T [auth C],
Z [auth D]
ERGOSTEROL
C28 H44 O
DNVPQKQSNYMLRS-APGDWVJJSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1

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: 2024-01-10
    Type: Initial release
  • Version 1.1: 2024-02-14
    Changes: Database references