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

    Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA.,Graduate Group in Biophysics, University of California, San Francisco, San Francisco, California, USA.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, Washington, USA.,Institute for Protein Design, Seattle, Washington, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.,Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA.,Department of Biochemistry, University of Washington, Seattle, Washington, 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