8FFO

Cryo-EM structure of wildtype rabbit TRPV5 with PI(4,5)P2 in nanodiscs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural basis of the activation of TRPV5 channels by long-chain acyl-Coenzyme-A.

Lee, B.H.De Jesus Perez, J.J.Moiseenkova-Bell, V.Rohacs, T.

(2023) Nat Commun 14: 5883-5883

  • DOI: https://doi.org/10.1038/s41467-023-41577-z
  • Primary Citation of Related Structures:  
    8FFO, 8FHH, 8FHI

  • PubMed Abstract: 

    Long-chain acyl-coenzyme A (LC-CoA) is a crucial metabolic intermediate that plays important cellular regulatory roles, including activation and inhibition of ion channels. The structural basis of ion channel regulation by LC-CoA is not known. Transient receptor potential vanilloid 5 and 6 (TRPV5 and TRPV6) are epithelial calcium-selective ion channels. Here, we demonstrate that LC-CoA activates TRPV5 and TRPV6 in inside-out patches, and both exogenously supplied and endogenously produced LC-CoA can substitute for the natural ligand phosphatidylinositol 4,5-bisphosphate (PI(4,5)P 2 ) in maintaining channel activity in intact cells. Utilizing cryo-electron microscopy, we determined the structure of LC-CoA-bound TRPV5, revealing an open configuration with LC-CoA occupying the same binding site as PI(4,5)P 2 in previous studies. This is consistent with our finding that PI(4,5)P 2 could not further activate the channels in the presence of LC-CoA. Our data provide molecular insights into ion channel regulation by a metabolic signaling molecule.


  • Organizational Affiliation

    Department of Pharmacology, Physiology and Neuroscience, Rutgers, New Jersey Medical School, Newark, NJ, USA.


Macromolecules
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 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CPL
Query on CPL

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
DA [auth D]
F [auth A]
G [auth A]
BA [auth D],
CA [auth D],
DA [auth D],
F [auth A],
G [auth A],
H [auth A],
K [auth A],
L [auth B],
N [auth B],
O [auth B],
P [auth B],
S [auth C],
U [auth C],
V [auth C],
W [auth C],
Z [auth D]
1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C42 H80 N O8 P
JLPULHDHAOZNQI-ZTIMHPMXSA-N
PIO (Subject of Investigation/LOI)
Query on PIO

Download Ideal Coordinates CCD File 
FA [auth D],
J [auth A],
R [auth B],
Y [auth C]
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
C25 H49 O19 P3
XLNCEHRXXWQMPK-MJUMVPIBSA-N
ERG
Query on ERG

Download Ideal Coordinates CCD File 
AA [auth D]
E [auth A]
EA [auth D]
I [auth A]
M [auth B]
AA [auth D],
E [auth A],
EA [auth D],
I [auth A],
M [auth B],
Q [auth B],
T [auth C],
X [auth C]
ERGOSTEROL
C28 H44 O
DNVPQKQSNYMLRS-APGDWVJJSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1
RECONSTRUCTIONcryoSPARC4.0.1

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: 2023-11-01
    Type: Initial release