3J9J

Structure of the capsaicin receptor, TRPV1, determined by single particle electron cryo-microscopy


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.275 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy.

Barad, B.A.Echols, N.Wang, R.Y.Cheng, Y.DiMaio, F.Adams, P.D.Fraser, J.S.

(2015) Nat.Methods 12: 943-946

  • DOI: 10.1038/nmeth.3541

  • PubMed Abstract: 
  • Advances in high-resolution cryo-electron microscopy (cryo-EM) require the development of validation metrics to independently assess map quality and model geometry. We report EMRinger, a tool that assesses the precise fitting of an atomic model into ...

    Advances in high-resolution cryo-electron microscopy (cryo-EM) require the development of validation metrics to independently assess map quality and model geometry. We report EMRinger, a tool that assesses the precise fitting of an atomic model into the map during refinement and shows how radiation damage alters scattering from negatively charged amino acids. EMRinger (https://github.com/fraser-lab/EMRinger) will be useful for monitoring progress in resolving and modeling high-resolution features in cryo-EM.


    Related Citations: 
    • Structure of the TRPV1 ion channel determined by electron cryo-microscopy.
      Liao, M.,Cao, E.,Julius, D.,Cheng, Y.
      (2013) Nature 504: 107


    Organizational Affiliation

    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, 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
586Rattus norvegicusMutation(s): 0 
Gene Names: Trpv1 (Vr1, Vr1l)
Find proteins for O35433 (Rattus norvegicus)
Go to UniProtKB:  O35433
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.275 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-02
    Type: Initial release
  • Version 1.1: 2015-10-14
    Type: Database references