3J9J

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 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
  • Primary Citation of Related Structures:  
    3J9J

  • 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 the map during refinement and shows how radiation damage alters scattering from negatively charged amino acids ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transient receptor potential cation channel subfamily V member 1A, B, C, D586Rattus norvegicusMutation(s): 0 
Gene Names: Trpv1Vr1Vr1l
Membrane Entity: Yes 
UniProt
Find proteins for O35433 (Rattus norvegicus)
Explore O35433 
Go to UniProtKB:  O35433
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO35433
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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