3J9J

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

PDB DOI: https://doi.org/10.2210/pdb3J9J/pdb
EM Map EMD-5778: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Rattus norvegicus
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2015-02-02 Released: 2015-09-02
Deposition Author(s): Wang, R.Y.-R., Barad, B.A., Fraser, J.S., DiMaio, F.

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 1.2 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

PubMed: 26280328 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/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. EMRinger (https://github.com/fraser-lab/EMRinger) will be useful for monitoring progress in resolving and modeling high-resolution features in cryo-EM.

Organizational Affiliation

Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.

Macromolecule Content

Total Structure Weight: 268.94 kDa
Atom Count: 10,444
Modelled Residue Count: 1,260
Deposited Residue Count: 2,344
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transient receptor potential cation channel subfamily V member 1	A, B, C, D	586	Rattus norvegicus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for O35433 (Rattus norvegicus) Explore O35433 Go to UniProtKB: O35433
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O35433
Sequence Annotations Expand
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

Released Date: 2015-09-02

Deposition Author(s):

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
Version 1.2: 2024-02-21
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.