7LP9

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.63 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

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

  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transient receptor potential cation channel subfamily V member 1
A, B, C, D
868Rattus norvegicusMutation(s): 0 
Gene Names: Trpv1Vr1Vr1l
Membrane Entity: Yes 
UniProt
Find proteins for O35433 (Rattus norvegicus)
Explore O35433 
Go to UniProtKB:  O35433
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO35433
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
T7X
Query on T7X

Download Ideal Coordinates CCD File 
E [auth A],
EA [auth C],
QA [auth D],
T [auth B]
Phosphatidylinositol
C47 H83 O13 P
KRTOMQDUKGRFDJ-TWUHCGEESA-N
LBN
Query on LBN

Download Ideal Coordinates CCD File 
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
YFP
Query on YFP

Download Ideal Coordinates CCD File 
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
6OU
Query on 6OU

Download Ideal Coordinates CCD File 
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
NA
Query on NA

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.63 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1.0
MODEL REFINEMENTPHENIX1.18.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR35NS097241

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-28
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references, Refinement description