6EID

Crystal structure of wild-type Channelrhodopsin 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural insights into ion conduction by channelrhodopsin 2.

Volkov, O.Kovalev, K.Polovinkin, V.Borshchevskiy, V.Bamann, C.Astashkin, R.Marin, E.Popov, A.Balandin, T.Willbold, D.Buldt, G.Bamberg, E.Gordeliy, V.

(2017) Science 358

  • DOI: https://doi.org/10.1126/science.aan8862
  • Primary Citation of Related Structures:  
    6EID, 6EIG

  • PubMed Abstract: 

    The light-gated ion channel channelrhodopsin 2 (ChR2) from Chlamydomonas reinhardtii is a major optogenetic tool. Photon absorption starts a well-characterized photocycle, but the structural basis for the regulation of channel opening remains unclear. We present high-resolution structures of ChR2 and the C128T mutant, which has a markedly increased open-state lifetime. The structure reveals two cavities on the intracellular side and two cavities on the extracellular side. They are connected by extended hydrogen-bonding networks involving water molecules and side-chain residues. Central is the retinal Schiff base that controls and synchronizes three gates that separate the cavities. Separate from this network is the DC gate that comprises a water-mediated bond between C128 and D156 and interacts directly with the retinal Schiff base. Comparison with the C128T structure reveals a direct connection of the DC gate to the central gate and suggests how the gating mechanism is affected by subtle tuning of the Schiff base's interactions.


  • Organizational Affiliation

    Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Archaeal-type opsin 2
A, B
315Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: cop4acop2COP4CSOBCHLREDRAFT_182032
Membrane Entity: Yes 
UniProt
Find proteins for Q8RUT8 (Chlamydomonas reinhardtii)
Explore Q8RUT8 
Go to UniProtKB:  Q8RUT8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8RUT8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
EDT
Query on EDT

Download Ideal Coordinates CCD File 
M [auth A]{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID
C10 H16 N2 O8
KCXVZYZYPLLWCC-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
K [auth A],
L [auth A],
S [auth B],
T [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LYR
Query on LYR
A, B
L-PEPTIDE LINKINGC26 H42 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.78α = 90
b = 135.77β = 92.95
c = 78.12γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata processing
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-15-CE11-0029- 02
Russian Science FoundationRussian Federation16-15-00242
French infrastructure for integrated structural biologyFranceANR-10-INSB-05- 02
GRALFranceANR-10-LABX- 49-01
German Research FoundationGermanyCEA(IBS)-HGF(FZJ) STC 5.1
German Research FoundationGermanySFB 807
ERA.Net RUS PlusRussian FederationID 323

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Author supporting evidence, Data collection, Database references, Refinement description