5IRX

Structure of TRPV1 in complex with DkTx and RTX, determined in lipid nanodisc


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.95 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transient receptor potential cation channel subfamily V member 1
A, B, C, D
636Rattus norvegicusMutation(s): 0 
Gene Names: Trpv1 (Vr1, Vr1l)
Membrane protein
mpstruct
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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tau-theraphotoxin-Hs1a
E, F
75Haplopelma schmidtiMutation(s): 0 
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Transient Receptor Potential (TRP)
Protein: 
TRPV1 transient receptor potential channel
Find proteins for P0CH43 (Haplopelma schmidti)
Go to UniProtKB:  P0CH43
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6OE
Query on 6OE

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

Download SDF File 
Download CCD File 
A, B, C, D
resiniferatoxin
RTX
C37 H40 O9
DSDNAKHZNJAGHN-MXTYGGKSSA-N
 Ligand Interaction
6O8
Query on 6O8

Download SDF File 
Download CCD File 
A, B, C, D
(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
6O9
Query on 6O9

Download SDF File 
Download CCD File 
D, E, F
(2S)-2-(acetyloxy)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}propyl pentanoate
C12 H24 N O8 P
PLBNSCVUDWCBFD-NSHDSACASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.95 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