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- PDB-6eid: Crystal structure of wild-type Channelrhodopsin 2 -

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Basic information

Entry
Database: PDB / ID: 6eid
TitleCrystal structure of wild-type Channelrhodopsin 2
ComponentsArchaeal-type opsin 2
KeywordsMEMBRANE PROTEIN / Retinal protein / Ion transport
Function / homologyBacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / plasma membrane / Chem-EDT / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PHOSPHATE ION / Archaeal-type opsin 2
Function and homology information
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsBorshchevskiy, V. / Kovalev, K. / Volkov, O. / Polovinkin, V. / Marin, E. / Balandin, T. / Astashkin, R. / Bamann, C. / Bueldt, G. / Willlbold, D. ...Borshchevskiy, V. / Kovalev, K. / Volkov, O. / Polovinkin, V. / Marin, E. / Balandin, T. / Astashkin, R. / Bamann, C. / Bueldt, G. / Willlbold, D. / Popov, A. / Bamberg, E. / Gordeliy, V.
Funding support France, Russian Federation, Germany, 7items
OrganizationGrant numberCountry
French National Research AgencyANR-15-CE11-0029- 02 France
Russian Science Foundation16-15-00242 Russian Federation
French infrastructure for integrated structural biologyANR-10-INSB-05- 02 France
GRALANR-10-LABX- 49-01 France
German Research FoundationCEA(IBS)-HGF(FZJ) STC 5.1 Germany
German Research FoundationSFB 807 Germany
ERA.Net RUS PlusID 323 Russian Federation
CitationJournal: Science / Year: 2017
Title: Structural insights into ion conduction by channelrhodopsin 2.
Authors: 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.
History
DepositionSep 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Archaeal-type opsin 2
B: Archaeal-type opsin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,70520
Polymers70,3982
Non-polymers5,30718
Water90150
1
A: Archaeal-type opsin 2
hetero molecules

A: Archaeal-type opsin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,06724
Polymers70,3982
Non-polymers6,66922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area5380 Å2
ΔGint-64 kcal/mol
Surface area21720 Å2
MethodPISA
2
B: Archaeal-type opsin 2
hetero molecules

B: Archaeal-type opsin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,34316
Polymers70,3982
Non-polymers3,94514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_658-x+1,y,-z+31
Buried area4420 Å2
ΔGint-63 kcal/mol
Surface area22210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.780, 135.770, 78.120
Angle α, β, γ (deg.)90.000, 92.950, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Archaeal-type opsin 2 / Chlamyopsin 4 light-gated ion channel / Retinal binding protein / Sensory opsin B


Mass: 35198.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: cop4, acop2, COP4, CSOB, CHLREDRAFT_182032 / Production host: Leishmania tarentolae (eukaryote) / References: UniProt: Q8RUT8
#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-EDT / {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID


Mass: 292.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O8
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.69 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: sodium potassium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 26159 / % possible obs: 100 % / Redundancy: 34.6 % / Rpim(I) all: 0.055 / Net I/σ(I): 8.3
Reflection shellResolution: 2.39→2.48 Å / Mean I/σ(I) obs: 1 / CC1/2: 0.182 / Rpim(I) all: 0.523

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0158refinement
BUSTERrefinement
PDB_EXTRACT3.22data extraction
XDSdata processing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UG9

3ug9


Resolution: 2.39→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.009 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.222
RfactorNum. reflection% reflectionSelection details
Rfree0.2193 1281 5 %RANDOM
Rwork0.2088 ---
obs0.2094 24535 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 153.39 Å2 / Biso mean: 67.203 Å2 / Biso min: 38.28 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å20 Å2-0.5 Å2
2---2.83 Å2-0 Å2
3---1.56 Å2
Refinement stepCycle: final / Resolution: 2.39→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3919 0 238 50 4207
Biso mean--84.76 61.82 -
Num. residues----498
LS refinement shellResolution: 2.39→2.451 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 100 -
Rwork0.455 1774 -
all-1874 -
obs--99.79 %

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