3UG9

Crystal Structure of the Closed State of Channelrhodopsin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal structure of the channelrhodopsin light-gated cation channel

Kato, H.E.Zhang, F.Yizhar, O.Ramakrishnan, C.Nishizawa, T.Hirata, K.Ito, J.Aita, Y.Tsukazaki, T.Hayashi, S.Hegemann, P.Maturana, A.D.Ishitani, R.Deisseroth, K.Nureki, O.

(2012) Nature 482: 369-374

  • DOI: 10.1038/nature10870

  • PubMed Abstract: 
  • Channelrhodopsins (ChRs) are light-gated cation channels derived from algae that have shown experimental utility in optogenetics; for example, neurons expressing ChRs can be optically controlled with high temporal precision within systems as complex ...

    Channelrhodopsins (ChRs) are light-gated cation channels derived from algae that have shown experimental utility in optogenetics; for example, neurons expressing ChRs can be optically controlled with high temporal precision within systems as complex as freely moving mammals. Although ChRs have been broadly applied to neuroscience research, little is known about the molecular mechanisms by which these unusual and powerful proteins operate. Here we present the crystal structure of a ChR (a C1C2 chimaera between ChR1 and ChR2 from Chlamydomonas reinhardtii) at 2.3 Å resolution. The structure reveals the essential molecular architecture of ChRs, including the retinal-binding pocket and cation conduction pathway. This integration of structural and electrophysiological analyses provides insight into the molecular basis for the remarkable function of ChRs, and paves the way for the precise and principled design of ChR variants with novel properties.


    Organizational Affiliation

    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Archaeal-type opsin 1, Archaeal-type opsin 2
A
333Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: cop4 (acop2, COP4, CSOB), acop1
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Bacterial and Algal Rhodopsins
Protein: 
Channelrhodopsin (ChR) chimera between ChR1 & ChR2
Find proteins for Q8RUT8 (Chlamydomonas reinhardtii)
Go to UniProtKB:  Q8RUT8
Find proteins for Q93WP2 (Chlamydomonas reinhardtii)
Go to UniProtKB:  Q93WP2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLA
Query on OLA

Download SDF File 
Download CCD File 
A
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
RET
Query on RET

Download SDF File 
Download CCD File 
A
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.204 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 59.471α = 90.00
b = 139.114β = 90.00
c = 90.049γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing
XDSdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-25
    Type: Initial release
  • Version 1.1: 2012-02-01
    Type: Database references
  • Version 1.2: 2012-02-22
    Type: Database references
  • Version 1.3: 2012-06-27
    Type: Structure summary
  • Version 1.4: 2017-08-09
    Type: Refinement description, Source and taxonomy