7RQZ | pdb_00007rqz

Cryo-EM structure of the full-length TRPV1 with RTx at 48 degrees Celsius, in an open state, class alpha

PDB DOI: https://doi.org/10.2210/pdb7RQZ/pdb
EM Map EMD-24641: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Rattus norvegicus
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes OPM PDBTM mpstruc

Deposited: 2021-08-08 Released: 2022-06-01
Deposition Author(s): Kwon, D.H., Suo, Y., Lee, S.-Y.
Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.32 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Vanilloid-dependent TRPV1 opening trajectory from cryoEM ensemble analysis.

Kwon, D.H., Zhang, F., Fedor, J.G., Suo, Y., Lee, S.Y.

(2022) Nat Commun 13: 2874-2874

PubMed: 35610228 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-022-30602-2
Primary Citation Related Structures:
7RQU, 7RQV, 7RQW, 7RQX, 7RQY, 7RQZ

PubMed Abstract:
Single particle cryo-EM often yields multiple protein conformations within a single dataset, but experimentally deducing the temporal relationship of these conformers within a conformational trajectory is not trivial. Here, we use thermal titration methods and cryo-EM in an attempt to obtain temporal resolution of the conformational trajectory of the vanilloid receptor TRPV1 with resiniferatoxin (RTx) bound. Based on our cryo-EM ensemble analysis, RTx binding to TRPV1 appears to induce intracellular gate opening first, followed by selectivity filter dilation, then pore loop rearrangement to reach the final open state. This apparent conformational wave likely arises from the concerted, stepwise, additive structural changes of TRPV1 over many subdomains. Greater understanding of the RTx-mediated long-range allostery of TRPV1 could help further the therapeutic potential of RTx, which is a promising drug candidate for pain relief associated with advanced cancer or knee arthritis.

Organizational Affiliation

Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA.

Macromolecule Content

Total Structure Weight: 409.22 kDa
Atom Count: 17,132
Modeled Residue Count: 2,128
Deposited Residue Count: 3,472
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 1	A, B [auth C], C [auth B], D	868	Rattus norvegicus	Mutation(s): 0 Gene Names: Trpv1, Vr1, Vr1l Membrane Entity: Yes
UniProt
Find proteins for O35433 (Rattus norvegicus) Explore O35433 Go to UniProtKB: O35433
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O35433
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LBN Query on LBN Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain T [auth D] SDF format, chain S [auth B] SDF format, chain P [auth B] SDF format, chain N [auth C] SDF format, chain K [auth C] SDF format, chain I [auth A] SDF format, chain F [auth A] MOL2 format, chain V [auth D] MOL2 format, chain T [auth D] MOL2 format, chain S [auth B] MOL2 format, chain P [auth B] MOL2 format, chain N [auth C] MOL2 format, chain K [auth C] MOL2 format, chain I [auth A] MOL2 format, chain F [auth A] mmCIF format, chain V [auth D] mmCIF format, chain T [auth D] mmCIF format, chain S [auth B] mmCIF format, chain P [auth B] mmCIF format, chain N [auth C] mmCIF format, chain K [auth C] mmCIF format, chain I [auth A] mmCIF format, chain F [auth A]	F [auth A] I [auth A] K [auth C] N [auth C] P [auth B] F [auth A], I [auth A], K [auth C], N [auth C], P [auth B], S [auth B], T [auth D], V [auth D]	1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-VYOBOKEXSA-N		Interactions Focus chain F [auth A] Focus chain I [auth A] Focus chain K [auth C] Focus chain N [auth C] Focus chain P [auth B] Focus chain S [auth B] Focus chain T [auth D] Focus chain V [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth A] Focus chain K [auth C] Focus chain N [auth C] Focus chain P [auth B] Focus chain S [auth B] Focus chain T [auth D] Focus chain V [auth D]
6OU Query on 6OU Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] L [auth C] M [auth C] Q [auth B] G [auth A], H [auth A], L [auth C], M [auth C], Q [auth B], R [auth B], W [auth D], X [auth D]	[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate C₃₉ H₇₆ N O₈ P FHQVHHIBKUMWTI-OTMQOFQLSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth C] Focus chain M [auth C] Focus chain Q [auth B] Focus chain R [auth B] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth C] Focus chain M [auth C] Focus chain Q [auth B] Focus chain R [auth B] Focus chain W [auth D] Focus chain X [auth D]
6EU Query on 6EU Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain O [auth B] SDF format, chain J [auth C] SDF format, chain E [auth A] MOL2 format, chain U [auth D] MOL2 format, chain O [auth B] MOL2 format, chain J [auth C] MOL2 format, chain E [auth A] mmCIF format, chain U [auth D] mmCIF format, chain O [auth B] mmCIF format, chain J [auth C] mmCIF format, chain E [auth A]	E [auth A], J [auth C], O [auth B], U [auth D]	resiniferatoxin C₃₇ H₄₀ O₉ DSDNAKHZNJAGHN-MXTYGGKSSA-N		Interactions Focus chain E [auth A] Focus chain J [auth C] Focus chain O [auth B] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth C] Focus chain O [auth B] Focus chain U [auth D]