8U2Z | pdb_00008u2z

TRPV1 in nanodisc bound with diC8-PIP2 in the dilated state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8U2Z

This is version 1.4 of the entry. See complete history

Literature

Structural basis of TRPV1 modulation by endogenous bioactive lipids.

Arnold, W.R.Mancino, A.Moss 3rd, F.R.Frost, A.Julius, D.Cheng, Y.

(2024) Nat Struct Mol Biol 31: 1377-1385

  • DOI: https://doi.org/10.1038/s41594-024-01299-2
  • Primary Citation Related Structures: 
    8T0C, 8T0E, 8T0Y, 8T10, 8T3L, 8T3M, 8U2Z, 8U30, 8U3A, 8U3C, 8U3J, 8U3L, 8U43, 8U4D

  • PubMed Abstract: 

    TRP ion channels are modulated by phosphoinositide lipids, but the underlying structural mechanisms remain unclear. The capsaicin- and heat-activated receptor, TRPV1, has served as a model for deciphering lipid modulation, which is relevant to understanding how pro-algesic agents enhance channel activity in the setting of inflammatory pain. Identification of a pocket within the TRPV1 transmembrane core has provided initial clues as to how phosphoinositide lipids bind to and regulate the channel. Here we show that this regulatory pocket in rat TRPV1 can accommodate diverse lipid species, including the inflammatory lipid lysophosphatidic acid, whose actions are determined by their specific modes of binding. Furthermore, we show that an empty-pocket channel lacking an endogenous phosphoinositide lipid assumes an agonist-like state, even at low temperature, substantiating the concept that phosphoinositide lipids serve as negative TRPV1 modulators whose ejection from the binding pocket is a critical step toward activation by thermal or chemical stimuli.


  • Organizational Affiliation
    • Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 299.26 kDa 
  • Atom Count: 17,045 
  • Modeled Residue Count: 2,040 
  • Deposited Residue Count: 2,540 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transient receptor potential cation channel subfamily V member 1A,
B [auth D],
C [auth B],
D [auth C]
635Rattus norvegicusMutation(s): 0 
Gene Names: Trpv1
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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PCW

Query on PCW



Download:Ideal Coordinates CCD File
F [auth A],
L [auth B],
M [auth B],
O [auth C]
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O
PIO
(Subject of Investigation/LOI)

Query on PIO



Download:Ideal Coordinates CCD File
E [auth A],
J [auth D],
K [auth B],
Q [auth C]
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
C25 H49 O19 P3
XLNCEHRXXWQMPK-MJUMVPIBSA-N
CLR

Query on CLR



Download:Ideal Coordinates CCD File
G [auth A],
I [auth D],
N [auth B],
P [auth C]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
H [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-08
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Database references
  • Version 1.2: 2024-09-25
    Changes: Data collection, Database references
  • Version 1.3: 2024-10-02
    Changes: Data collection, Database references
  • Version 1.4: 2025-05-14
    Changes: Data collection, Structure summary