RCSB PDB - 9GO2: C1C2 Channelrhodopsin - SMX Light activated structure

 9GO2

C1C2 Channelrhodopsin - SMX Light activated structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

Structural Insights Into the Opening Mechanism of C1C2 Channelrhodopsin.

Mulder, M.Hwang, S.Broser, M.Brunle, S.Skopintsev, P.Schattenberg, C.Schnick, C.Hartmann, S.Church, J.Schapiro, I.Dworkowski, F.Weinert, T.Hegemann, P.Sun, H.Standfuss, J.

(2025) J Am Chem Soc 147: 1282-1290

  • DOI: https://doi.org/10.1021/jacs.4c15402
  • Primary Citation of Related Structures:  
    9GO1, 9GO2

  • PubMed Abstract: 

    Channelrhodopsins, light-gated cation channels, enable precise control of neural cell depolarization or hyperpolarization with light in the field of optogenetics. This study integrates time-resolved serial crystallography and atomistic molecular dynamics (MD) simulations to resolve the structural changes during C1C2 channelrhodopsin activation. Our observations reveal that within the crystal environment, C1C2 predominantly remains in a light-activated state with characteristics of the M 390 intermediate. Here, rearrangement of retinal within its binding pocket partially opens the central gate toward the extracellular vestibule. These structural changes initiate channel opening but were insufficient to allow K + flow. Adjusting protonation states to represent the subsequent N 520 intermediate in our MD simulations induced further conformational changes, including rearrangements of transmembrane helices 2 and 7, that opened the inner gate and the putative ion-translocation pathway. This allowed spontaneous cation conduction with low conductance, aligning with experimental findings. Our findings provide critical structural insights into key intermediates of the channel opening mechanism, enhancing our understanding of ion conduction and selectivity in channelrhodopsins at an atomistic level.


  • Organizational Affiliation

    PSI Center for Life Sciences, Laboratory for Biomolecular Research, Paul Scherrer Institut, Villigen 5232, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Archaeal-type opsin 1,Archaeal-type opsin 2333Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: acop1cop4acop2CSOBCHLRE_02g085257v5
UniProt
Find proteins for Q93WP2 (Chlamydomonas reinhardtii)
Explore Q93WP2 
Go to UniProtKB:  Q93WP2
Find proteins for Q8RUT8 (Chlamydomonas reinhardtii)
Explore Q8RUT8 
Go to UniProtKB:  Q8RUT8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ8RUT8Q93WP2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
RET (Subject of Investigation/LOI)
Query on RET

Download Ideal Coordinates CCD File 
K [auth A]RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.4α = 90
b = 141.7β = 90
c = 94.4γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted RETClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland310030_197674
Swiss National Science FoundationSwitzerland310030_207462
InnosuisseEuropean Union42711.1 IP-LS

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release