5IS0

Structure of TRPV1 in complex with capsazepine, determined in lipid nanodisc

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

  • 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: 3.43 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 ...

    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 1BCDE636Rattus norvegicusMutation(s): 0 
Gene Names: Trpv1Vr1Vr1l
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Transient Receptor Potential (TRP)
Protein: 
TRPV1 transient receptor potential channel in nanodiscs
Find proteins for O35433 (Rattus norvegicus)
Explore O35433 
Go to UniProtKB:  O35433
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6ET
Query on 6ET

Download CCD File 
B, C, D, E
capsazepine
C19 H21 Cl N2 O2 S
DRCMAZOSEIMCHM-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6ETIC50:  3   nM  BindingDB
6ETIC50:  39   nM  BindingDB
6ETIC50:  4   nM  BindingDB
6ETIC50:  68   nM  BindingDB
6ETIC50:  69   nM  BindingDB
6ETIC50:  56   nM  BindingDB
6ETKi:  1288   nM  BindingDB
6ETIC50:  53   nM  BindingDB
6ETKi:  4300   nM  BindingDB
6ETIC50:  220   nM  BindingDB
6ETEC50:  520   nM  BindingDB
6ETIC50:  420   nM  BindingDB
6ETIC50:  320   nM  BindingDB
6ETIC50:  590   nM  BindingDB
6ETIC50:  334   nM  BindingDB
6ETIC50:  600   nM  BindingDB
6ETIC50:  365   nM  BindingDB
6ETKi:  520   nM  BindingDB
6ETIC50:  887   nM  BindingDB
6ETKi:  1200   nM  BindingDB
6ETIC50:  58   nM  BindingDB
6ETKi:  1300   nM  BindingDB
6ETIC50:  4   nM  BindingDB
6ETIC50:  2600   nM  BindingDB
6ETIC50:  150   nM  BindingDB
6ETEC50:  100000   nM  BindingDB
6ETIC50:  650   nM  BindingDB
6ETEC50:  32   nM  BindingDB
6ETKi:  120   nM  BindingDB
6ETIC50:  100   nM  BindingDB
6ETIC50:  5   nM  BindingDB
6ETIC50:  74   nM  BindingDB
6ETEC50:  2511.889892578125   nM  BindingDB
6ETIC50:  30000   nM  BindingDB
6ETEC50:  282   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.43 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 

  • 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