8FHI | pdb_00008fhi

Wildtype rabbit TRPV5 in nanodiscs in complex with oleoyl coenzyme A, Open stated

PDB DOI: https://doi.org/10.2210/pdb8FHI/pdb
EM Map EMD-29086: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Oryctolagus cuniculus
Expression System: Saccharomyces cerevisiae
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD mpstruc

Deposited: 2022-12-14 Released: 2023-11-01
Deposition Author(s): De Jesus-Perez, J.J., Moiseenkova-Bell, V.Y.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.25 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

PubMed: 37735536 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-023-41577-z
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 345.48 kDa
Atom Count: 20,116
Modeled Residue Count: 2,440
Deposited Residue Count: 2,956
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transient receptor potential cation channel subfamily V member 5	A, B, C, D	739	Oryctolagus cuniculus	Mutation(s): 0 Gene Names: Trpv5, Ecac1 Membrane Entity: Yes
UniProt
Find proteins for Q9XSM3 (Oryctolagus cuniculus) Explore Q9XSM3 Go to UniProtKB: Q9XSM3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9XSM3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3VV (Subject of Investigation/LOI) Query on 3VV Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain O [auth C] SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain T [auth D] MOL2 format, chain O [auth C] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain T [auth D] mmCIF format, chain O [auth C] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	G [auth A], K [auth B], O [auth C], T [auth D]	S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (9Z)-octadec-9-enethioate (non-preferred name) C₃₉ H₆₈ N₇ O₁₇ P₃ S XDUHQPOXLUAVEE-BPMMELMSSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain T [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain T [auth D]
POV Query on POV Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain P [auth C] SDF format, chain L [auth B] SDF format, chain H [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth C] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth C] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A]	H [auth A], L [auth B], P [auth C], Q [auth D]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-PFDVCBLKSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth D] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth D]
ERG Query on ERG Download:Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] I [auth B] J [auth B] M [auth C] E [auth A], F [auth A], I [auth B], J [auth B], M [auth C], N [auth C], R [auth D], S [auth D]	ERGOSTEROL C₂₈ H₄₄ O DNVPQKQSNYMLRS-APGDWVJJSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain R [auth D] Focus chain S [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.25 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.0.2
MODEL REFINEMENT	PHENIX	1.20.1

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-11-01

Deposition Author(s):

De Jesus-Perez, J.J.

Moiseenkova-Bell, V.Y.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM144120
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM093290