5IRZ

Structure of TRPV1 determined in lipid nanodisc

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

  • 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 (NIH/NINDS), National Institutes of Health/Office of the Director, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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 1.4 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:  
    5IRX, 5IRZ, 5IS0

  • 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 lipids have both structural and regulatory roles ...

    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

    Howard Hughes Medical Institute, University of California, San Francisco, California 94143, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transient receptor potential cation channel subfamily V member 1C [auth B], D [auth C], A [auth D], B [auth E]636Rattus norvegicusMutation(s): 0 
Gene Names: Trpv1Vr1Vr1l
Membrane Entity: Yes 
UniProt
Find proteins for O35433 (Rattus norvegicus)
Explore O35433 
Go to UniProtKB:  O35433
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6ES
Query on 6ES

Download Ideal Coordinates CCD File 
F [auth D], L [auth E], R [auth B], X [auth C](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
6O8
Query on 6O8

Download Ideal Coordinates CCD File 
E [auth D], K [auth E], Q [auth B], W [auth C](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
6OE
Query on 6OE

Download Ideal Coordinates CCD File 
AA [auth C] , BA [auth C] , G [auth D] , H [auth D] , I [auth D] , J [auth D] , M [auth E] , N [auth E] , 
AA [auth C],  BA [auth C],  G [auth D],  H [auth D],  I [auth D],  J [auth D],  M [auth E],  N [auth E],  O [auth E],  P [auth E],  S [auth B],  T [auth B],  U [auth B],  V [auth B],  Y [auth C],  Z [auth C]
(2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl hexanoate
C17 H34 N O8 P
PELYUHWUVHDSSU-HNNXBMFYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 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 Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01NS047723
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR37NS065071
National Institutes of Health/Office of the DirectorUnited StatesS10OD020054
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM098672

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-25
    Type: Initial release
  • Version 1.1: 2016-06-22
    Changes: Database references
  • Version 1.2: 2016-11-30
    Changes: Source and taxonomy
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2019-12-18
    Changes: Author supporting evidence