6L93

X-ray structure of the ligand-free human TRPV1 ankyrin repeat domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.47 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure determination of the human TRPV1 ankyrin-repeat domain under nonreducing conditions.

Tanaka, M.Hayakawa, K.Ogawa, N.Kurokawa, T.Kitanishi, K.Ite, K.Matsui, T.Mori, Y.Unno, M.

(2020) Acta Crystallogr F Struct Biol Commun 76: 130-137

  • DOI: https://doi.org/10.1107/S2053230X20001533
  • Primary Citation of Related Structures:  
    6L93

  • PubMed Abstract: 

    TRPV1, a member of the transient receptor potential (TRP) channels family, has been found to be involved in redox sensing. The crystal structure of the human TRPV1 ankyrin-repeat domain (TRPV1-ARD) was determined at 4.5 Å resolution under nonreducing conditions. This is the first report of the crystal structure of a ligand-free form of TRPV1-ARD and in particular of the human homologue. The structure showed a unique conformation in finger loop 3 near Cys258, which is most likely to be involved in inter-subunit disulfide-bond formation. Also, in human TRPV1-ARD it was possible for solvent to access Cys258. This structural feature might be related to the high sensitivity of human TRPV1 to oxidants. ESI-MS revealed that Cys258 did not form an S-OH functionality even under nonreducing conditions.


  • Organizational Affiliation

    Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki 316-8511, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transient receptor potential cation channel subfamily V member 1
A, B, C, D, E
A, B, C, D, E, F
280Homo sapiensMutation(s): 0 
Gene Names: TRPV1VR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NER1 (Homo sapiens)
Explore Q8NER1 
Go to UniProtKB:  Q8NER1
PHAROS:  Q8NER1
GTEx:  ENSG00000196689 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NER1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.47 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.228α = 90
b = 167.414β = 108.375
c = 112.632γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description