7LR0

Structure of squirrel TRPV1 in complex with capsaicin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.81 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

Extracellular cap domain is an essential component of the TRPV1 gating mechanism.

Nadezhdin, K.D.Neuberger, A.Nikolaev, Y.A.Murphy, L.A.Gracheva, E.O.Bagriantsev, S.N.Sobolevsky, A.I.

(2021) Nat Commun 12: 2154-2154

  • DOI: 10.1038/s41467-021-22507-3
  • Primary Citation of Related Structures:  
    7LQY, 7LQZ, 7LR0

  • PubMed Abstract: 
  • Transient receptor potential (TRP) channels are polymodal molecular sensors involved in numerous physiological processes and implicated in a variety of human diseases. Several structures of the founding member of the TRP channel family, TRPV1, are available, all of which were determined for the protein missing the N- and C-termini and the extracellular S5-P-loop ...

    Transient receptor potential (TRP) channels are polymodal molecular sensors involved in numerous physiological processes and implicated in a variety of human diseases. Several structures of the founding member of the TRP channel family, TRPV1, are available, all of which were determined for the protein missing the N- and C-termini and the extracellular S5-P-loop. Here, we present structures of the full-length thirteen-lined ground squirrel TRPV1 solved by cryo-EM. Our structures resolve the extracellular cap domain formed by the S5-P-loops and the C-terminus that wraps around the three-stranded β-sheet connecting elements of the TRPV1 intracellular skirt. The cap domain forms a dome above the pore's extracellular entrance, with four portals leading to the ion conductance pathway. Deletion of the cap increases the TRPV1 average conductance, reduces the open probability and affects ion selectivity. Our data show that both the termini and the cap domain are critical determinants of TRPV1 function.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA. as4005@cumc.columbia.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Osm-9-like TRP channel 1A, B, C, D844Ictidomys tridecemlineatusMutation(s): 0 
Gene Names: TRPV1
Membrane Entity: Yes 
UniProt
Find proteins for I3LZN5 (Ictidomys tridecemlineatus)
Explore I3LZN5 
Go to UniProtKB:  I3LZN5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POV (Subject of Investigation/LOI)
Query on POV

Download Ideal Coordinates CCD File 
AA [auth C] , BA [auth C] , CA [auth C] , DA [auth C] , E [auth A] , EA [auth D] , F [auth A] , FA [auth D] , 
AA [auth C],  BA [auth C],  CA [auth C],  DA [auth C],  E [auth A],  EA [auth D],  F [auth A],  FA [auth D],  GA [auth D],  H [auth A],  I [auth A],  IA [auth D],  J [auth A],  JA [auth D],  K [auth A],  KA [auth D],  L [auth A],  M [auth A],  O [auth B],  P [auth B],  R [auth B],  S [auth B],  T [auth B],  U [auth B],  V [auth B],  W [auth C],  X [auth C],  Z [auth C]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
 Ligand Interaction
4DY (Subject of Investigation/LOI)
Query on 4DY

Download Ideal Coordinates CCD File 
G [auth A], HA [auth D], Q [auth B], Y [auth C](6E)-N-(4-hydroxy-3-methoxybenzyl)-8-methylnon-6-enamide
C18 H27 N O3
YKPUWZUDDOIDPM-SOFGYWHQSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
N [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.81 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA206573
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01 NS083660
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01 NS107253
National Science Foundation (NSF, United States)United States1818086

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-21
    Type: Initial release
  • Version 1.1: 2021-04-28
    Changes: Database references