5ZIH

Crystal structure of the red light-activated channelrhodopsin Chrimson.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of the red light-activated channelrhodopsin Chrimson.

Oda, K.Vierock, J.Oishi, S.Rodriguez-Rozada, S.Taniguchi, R.Yamashita, K.Wiegert, J.S.Nishizawa, T.Hegemann, P.Nureki, O.

(2018) Nat Commun 9: 3949-3949

  • DOI: 10.1038/s41467-018-06421-9
  • Primary Citation of Related Structures:  
    5ZIH

  • PubMed Abstract: 
  • Channelrhodopsins are light-activated ion channels that mediate cation permeation across cell membranes upon light absorption. Red-light-activated channelrhodopsins are of particular interest, because red light penetrates deeper into biological tissu ...

    Channelrhodopsins are light-activated ion channels that mediate cation permeation across cell membranes upon light absorption. Red-light-activated channelrhodopsins are of particular interest, because red light penetrates deeper into biological tissues and also enables dual-color experiments in combination with blue-light-activated optogenetic tools. Here we report the crystal structure of the most red-shifted channelrhodopsin from the algae Chlamydomonas noctigama, Chrimson, at 2.6 Å resolution. Chrimson resembles prokaryotic proton pumps in the retinal binding pocket, while sharing similarity with other channelrhodopsins in the ion-conducting pore. Concomitant mutation analysis identified the structural features that are responsible for Chrimson's red light sensitivity; namely, the protonation of the counterion for the retinal Schiff base, and the polar residue distribution and rigidity of the retinal binding pocket. Based on these mechanistic insights, we engineered ChrimsonSA, a mutant with a maximum activation wavelength red-shifted beyond 605 nm and accelerated closing kinetics.


    Organizational Affiliation

    Department of Biological Sciences Graduate School of Science, The University of Tokyo, Tokyo, 113-0034, Japan. nureki@bs.s.u-tokyo.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sensory opsin A,ChrimsonAB347Chlamydomonas reinhardtiiChlamydomonas noctigama
This entity is chimeric
Mutation(s): 0 
Gene Names: CSOA
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Bacterial, Algal, and viral Rhodopsins
Protein: 
Channelrhodopsin Chrimson
Find proteins for Q8L435 (Chlamydomonas reinhardtii)
Explore Q8L435 
Go to UniProtKB:  Q8L435
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download CCD File 
A, B
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LYR
Query on LYR
A,BL-PEPTIDE LINKINGC26 H42 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.233 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.99α = 90
b = 81.44β = 90
c = 170.14γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
MEXTJapan16H06294
JSTJapanJPMJPR14L8

Revision History 

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2018-11-28
    Changes: Data collection, Database references