Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 250 microsecond structure

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.514 
  • R-Value Work: 0.447 
  • R-Value Observed: 0.450 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin.

Oda, K.Nomura, T.Nakane, T.Yamashita, K.Inoue, K.Ito, S.Vierock, J.Hirata, K.Maturana, A.D.Katayama, K.Ikuta, T.Ishigami, I.Izume, T.Umeda, R.Eguma, R.Oishi, S.Kasuya, G.Kato, T.Kusakizako, T.Shihoya, W.Shimada, H.Takatsuji, T.Takemoto, M.Taniguchi, R.Tomita, A.Nakamura, R.Fukuda, M.Miyauchi, H.Lee, Y.Nango, E.Tanaka, R.Tanaka, T.Sugahara, M.Kimura, T.Shimamura, T.Fujiwara, T.Yamanaka, Y.Owada, S.Joti, Y.Tono, K.Ishitani, R.Hayashi, S.Kandori, H.Hegemann, P.Iwata, S.Kubo, M.Nishizawa, T.Nureki, O.

(2021) Elife 10

  • DOI: https://doi.org/10.7554/eLife.62389
  • Primary Citation of Related Structures:  
    7C86, 7E6X, 7E6Y, 7E6Z, 7E70, 7E71

  • PubMed Abstract: 

    Channelrhodopsins (ChRs) are microbial light-gated ion channels utilized in optogenetics to control neural activity with light . Light absorption causes retinal chromophore isomerization and subsequent protein conformational changes visualized as optically distinguished intermediates, coupled with channel opening and closing. However, the detailed molecular events underlying channel gating remain unknown. We performed time-resolved serial femtosecond crystallographic analyses of ChR by using an X-ray free electron laser, which revealed conformational changes following photoactivation. The isomerized retinal adopts a twisted conformation and shifts toward the putative internal proton donor residues, consequently inducing an outward shift of TM3, as well as a local deformation in TM7. These early conformational changes in the pore-forming helices should be the triggers that lead to opening of the ion conducting pore.

  • Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Archaeal-type opsin 1,Archaeal-type opsin 2356Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: acop1cop4acop2COP4CSOBCHLRE_02g085257v5CHLREDRAFT_182032
Membrane Entity: Yes 
Find proteins for Q8RUT8 (Chlamydomonas reinhardtii)
Explore Q8RUT8 
Go to UniProtKB:  Q8RUT8
Find proteins for Q93WP2 (Chlamydomonas reinhardtii)
Explore Q93WP2 
Go to UniProtKB:  Q93WP2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ8RUT8Q93WP2
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB [auth E]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on OLC

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
Query on RET

Download Ideal Coordinates CCD File 
C20 H28 O
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.8α = 90
b = 142.2β = 90
c = 94.7γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History