5IRZ

Structure of TRPV1 determined in lipid nanodisc

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Rattus norvegicus
  • Expression System: Homo sapiens

  • Deposited: 2016-03-15 Released: 2016-05-25 
  • Deposition Author(s): Gao, Y., Cao, E., Julius, D., Cheng, Y.
  • Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke; National Institutes of Health/Office of the Director; National Institutes of Health/National Institute of General Medical Sciences 

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action.

Gao, Y.Cao, E.Julius, D.Cheng, Y.

(2016) Nature 534: 347-351

  • DOI: 10.1038/nature17964
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • When integral membrane proteins are visualized in detergents or other artificial systems, an important layer of information is lost regarding lipid interactions and their effects on protein structure. This is especially relevant to proteins for which ...

    When integral membrane proteins are visualized in detergents or other artificial systems, an important layer of information is lost regarding lipid interactions and their effects on protein structure. This is especially relevant to proteins for which lipids have both structural and regulatory roles. Here we demonstrate the power of combining electron cryo-microscopy with lipid nanodisc technology to ascertain the structure of the rat TRPV1 ion channel in a native bilayer environment. Using this approach, we determined the locations of annular and regulatory lipids and showed that specific phospholipid interactions enhance binding of a spider toxin to TRPV1 through formation of a tripartite complex. Furthermore, phosphatidylinositol lipids occupy the binding site for capsaicin and other vanilloid ligands, suggesting a mechanism whereby chemical or thermal stimuli elicit channel activation by promoting the release of bioactive lipids from a critical allosteric regulatory site.


    Organizational Affiliation

    Department of Physiology, University of California, San Francisco, California 94143, USA.,Keck Advanced Microscopy Laboratory and Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, USA.,Howard Hughes Medical Institute, University of California, San Francisco, California 94143, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transient receptor potential cation channel subfamily V member 1
D, E, B, C
636Rattus norvegicusMutation(s): 0 
Gene Names: Trpv1 (Vr1, Vr1l)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Transient Receptor Potential (TRP)
Protein: 
TRPV1 transient receptor potential channel
Find proteins for O35433 (Rattus norvegicus)
Go to UniProtKB:  O35433
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6OE
Query on 6OE

Download SDF File 
Download CCD File 
B, C, D, E
(2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl hexanoate
C17 H34 N O8 P
PELYUHWUVHDSSU-HNNXBMFYSA-N
 Ligand Interaction
6O8
Query on 6O8

Download SDF File 
Download CCD File 
B, C, D, E
(4R,7S)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(pentanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphatetradecan-1-aminium
C19 H39 N O8 P
IZTOQGOABQJQQN-KRWDZBQOSA-O
 Ligand Interaction
6ES
Query on 6ES

Download SDF File 
Download CCD File 
B, C, D, E
(2S)-1-{[(R)-hydroxy{[(1R,2R,3S,4S,5S,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}-3-(pentanoyloxy)propan-2-yl decanoate
C24 H45 O13 P
YWVFSDQOBMMIAJ-CLASQLQRSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and StrokeUnited StatesR01NS047723
National Institutes of Health/National Institute of Neurological Disorders and StrokeUnited StatesR37NS065071
National Institutes of Health/Office of the DirectorUnited StatesS10OD020054
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM098672

Revision History 

  • Version 1.0: 2016-05-25
    Type: Initial release
  • Version 1.1: 2016-06-22
    Type: Database references
  • Version 1.2: 2016-11-30
    Type: Source and taxonomy
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence, Data collection