3UG9

Crystal Structure of the Closed State of Channelrhodopsin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.209 

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
  • Primary Citation of Related Structures:  
    3UG9

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Archaeal-type opsin 1, Archaeal-type opsin 2A333Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: acop1acop2CHLREDRAFT_182032COP4CSOB
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Bacterial, Algal, and viral Rhodopsins
Protein: 
Channelrhodopsin (ChR) chimera between ChR1 & ChR2
Find proteins for Q93WP2 (Chlamydomonas reinhardtii)
Explore Q93WP2 
Go to UniProtKB:  Q93WP2
Find proteins for Q8RUT8 (Chlamydomonas reinhardtii)
Explore Q8RUT8 
Go to UniProtKB:  Q8RUT8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RET
Query on RET

Download CCD File 
A
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
OLA
Query on OLA

Download CCD File 
A
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.209 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.471α = 90
b = 139.114β = 90
c = 90.049γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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