7LP9

Cryo-EM structure of full-length TRPV1 at 4 degrees Celsius

PDB DOI: https://doi.org/10.2210/pdb7LP9/pdb
EM Map EMD-23473: EMDB EMDataResource

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

Deposited: 2021-02-11 Released: 2021-07-28
Deposition Author(s): Kwon, D.H., Zhang, F., 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: 2.63 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.

Literature

Heat-dependent opening of TRPV1 in the presence of capsaicin.

Kwon, D.H., Zhang, F., Suo, Y., Bouvette, J., Borgnia, M.J., Lee, S.Y.

(2021) Nat Struct Mol Biol 28: 554-563

PubMed: 34239123 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41594-021-00616-3
Primary Citation of Related Structures:
7LP9, 7LPA, 7LPB, 7LPC, 7LPD, 7LPE

PubMed Abstract:
Transient receptor potential vanilloid member 1 (TRPV1) is a Ca ²⁺-permeable cation channel that serves as the primary heat and capsaicin sensor in humans. Using cryo-EM, we have determined the structures of apo and capsaicin-bound full-length rat TRPV1 reconstituted into lipid nanodiscs over a range of temperatures. This has allowed us to visualize the noxious heat-induced opening of TRPV1 in the presence of capsaicin. Notably, noxious heat-dependent TRPV1 opening comprises stepwise conformational transitions. Global conformational changes across multiple subdomains of TRPV1 are followed by the rearrangement of the outer pore, leading to gate opening. Solvent-accessible surface area analyses and functional studies suggest that a subset of residues form an interaction network that is directly involved in heat sensing. Our study provides a glimpse of the molecular principles underlying noxious physical and chemical stimuli sensing by TRPV1, which can be extended to other thermal sensing ion channels.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 427.65 kDa
Atom Count: 20,977
Modelled Residue Count: 2,536
Deposited Residue Count: 3,472
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transient receptor potential cation channel subfamily V member 1	A, B, C, 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O35433
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
T7X Query on T7X Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain QA [auth D] SDF format, chain T [auth B] SDF format, chain E [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain QA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain E [auth A]	E [auth A], EA [auth C], QA [auth D], T [auth B]	Phosphatidylinositol C₄₇ H₈₃ O₁₃ P KRTOMQDUKGRFDJ-TWUHCGEESA-N		Interactions Focus chain E [auth A] Focus chain EA [auth C] Focus chain QA [auth D] Focus chain T [auth B] Interactions & Density Focus chain E [auth A] Focus chain EA [auth C] Focus chain QA [auth D] Focus chain T [auth B]
LBN Query on LBN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain FA [auth C] SDF format, chain N [auth A] SDF format, chain PA [auth D] SDF format, chain R [auth B] SDF format, chain RA [auth D] SDF format, chain U [auth B] SDF format, chain CA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain CA [auth C]	CA [auth C] F [auth A] FA [auth C] N [auth A] PA [auth D] CA [auth C], F [auth A], FA [auth C], N [auth A], PA [auth D], R [auth B], RA [auth D], U [auth B]	1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-VYOBOKEXSA-N		Interactions Focus chain CA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain N [auth A] Focus chain PA [auth D] Focus chain R [auth B] Focus chain RA [auth D] Focus chain U [auth B] Interactions & Density Focus chain CA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain N [auth A] Focus chain PA [auth D] Focus chain R [auth B] Focus chain RA [auth D] Focus chain U [auth B]
YFP Query on YFP Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain IA [auth C] SDF format, chain S [auth B] SDF format, chain UA [auth D] MOL2 format, chain DA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain S [auth B] MOL2 format, chain UA [auth D]	DA [auth C], IA [auth C], S [auth B], UA [auth D]	1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol C₄₀ H₇₇ O₁₀ P PAZGBAOHGQRCBP-YWIOZPJLSA-N		Interactions Focus chain DA [auth C] Focus chain IA [auth C] Focus chain S [auth B] Focus chain UA [auth D] Interactions & Density Focus chain DA [auth C] Focus chain IA [auth C] Focus chain S [auth B] Focus chain UA [auth D]
6OU Query on 6OU Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth C] SDF format, chain G [auth A] SDF format, chain GA [auth C] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain I [auth A] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain MA [auth C] SDF format, chain NA [auth D] SDF format, chain Q [auth B] SDF format, chain SA [auth D] SDF format, chain TA [auth D] SDF format, chain V [auth B] SDF format, chain VA [auth D] SDF format, chain W [auth B] SDF format, chain WA [auth D] SDF format, chain X [auth B] SDF format, chain XA [auth D] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain J [auth A] SDF format, chain M [auth A] SDF format, chain OA [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain NA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain SA [auth D] MOL2 format, chain TA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain J [auth A] MOL2 format, chain M [auth A] MOL2 format, chain OA [auth D]	AA [auth B] BA [auth C] G [auth A] GA [auth C] H [auth A] AA [auth B], BA [auth C], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], NA [auth D], OA [auth D], Q [auth B], SA [auth D], TA [auth D], V [auth B], VA [auth D], W [auth B], WA [auth D], X [auth B], XA [auth D], Y [auth B], Z [auth B]	[(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 AA [auth B] Focus chain BA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain Q [auth B] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain Q [auth B] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain Z [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A]	O [auth A], P [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain O [auth A] Focus chain P [auth A]