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- PDB-9go1: C1C2 Channelrhodopsin - SMX Dark structure -

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Basic information

Entry
Database: PDB / ID: 9go1
TitleC1C2 Channelrhodopsin - SMX Dark structure
ComponentsArchaeal-type opsin 1,Archaeal-type opsin 2
KeywordsMEMBRANE PROTEIN / channelrhodopsin / dark
Function / homology
Function and homology information


photoreceptor activity / phototransduction / membrane / plasma membrane
Similarity search - Function
Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Archaeal-type opsin 2 / Archaeal-type opsin 1
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsMulder, M. / Weinert, T. / Skopintsev, P. / Bruenle, S. / Broser, M. / Hegemann, P. / Standfuss, J.
Funding support Switzerland, European Union, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_197674 Switzerland
Swiss National Science Foundation310030_207462 Switzerland
Innosuisse42711.1 IP-LSEuropean Union
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Structural Insights Into the Opening Mechanism of C1C2 Channelrhodopsin.
Authors: 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. / ...Authors: 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.
History
DepositionSep 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Archaeal-type opsin 1,Archaeal-type opsin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,93511
Polymers37,4421
Non-polymers3,49310
Water23413
1
A: Archaeal-type opsin 1,Archaeal-type opsin 2
hetero molecules

A: Archaeal-type opsin 1,Archaeal-type opsin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,87122
Polymers74,8842
Non-polymers6,98720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area6140 Å2
ΔGint-54 kcal/mol
Surface area26280 Å2
Unit cell
Length a, b, c (Å)61.400, 141.700, 94.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2

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Components

#1: Protein Archaeal-type opsin 1,Archaeal-type opsin 2 / Channelopsin-1 / Retinal binding protein / Sensory opsin B


Mass: 37441.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: acop1, cop4, acop2, CSOB, CHLRE_02g085257v5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q93WP2, 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.: 9 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.72 Å3/Da / Density % sol: 54.82 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM sodium citrate (pH 6.0), 30% PEG500DME, 100 mM MgCl2, 100 mM NaCl, and 100 mM (NH4)2SO4.

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 7, 2019
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→70.85 Å / Num. obs: 8838 / % possible obs: 67.7 % / Redundancy: 415.94 % / CC star: 0.999 / R split: 0.06 / Net I/σ(I): 10.7
Reflection shellResolution: 2.59→2.69 Å / Mean I/σ(I) obs: 1.05 / Num. unique obs: 1288 / CC star: 0.849 / R split: 0.87
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
CrystFEL0.9.1data reduction
CrystFEL0.9.1.data scaling
PHENIX1.20_4459phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→70.85 Å / SU ML: 0.2925 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.8552
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2696 884 10 %
Rwork0.2114 7952 -
obs0.2171 8836 66.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.64 Å2
Refinement stepCycle: LAST / Resolution: 2.59→70.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2321 0 126 13 2460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00462499
X-RAY DIFFRACTIONf_angle_d0.91933363
X-RAY DIFFRACTIONf_chiral_restr0.0535371
X-RAY DIFFRACTIONf_plane_restr0.0035417
X-RAY DIFFRACTIONf_dihedral_angle_d11.9305422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.750.3509250.3251245X-RAY DIFFRACTION12.62
2.75-2.960.3137610.2929531X-RAY DIFFRACTION27.11
2.96-3.260.3631260.27041146X-RAY DIFFRACTION58.81
3.26-3.730.2882190.21761957X-RAY DIFFRACTION99.63
3.73-4.70.24632220.18111999X-RAY DIFFRACTION100
4.7-70.850.25632310.21272074X-RAY DIFFRACTION99.78
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.414046143198-0.1213619875210.07111596072640.0396207844912-0.01532025081810.0646154374888-0.0953775559794-0.103943142009-0.2221165564590.05987129938080.1268968305450.005944953055750.02188280382380.0207622362806-0.01596197035570.2065309868250.02596806478010.149238860540.201678731549-0.04384151743950.4383801402484.664946129413.9688064494619.5548052039
20.307864394053-0.004935323239010.4691766519990.0870776264746-0.09466943838580.81169763727-0.231199112677-0.144660151221-0.474638609318-0.0344934215317-0.19069660875-0.0934923445380.1743213564260.111720919632-0.2054350027760.416848554632-0.1015725585760.2899237832330.465604872682-0.09169640939940.75123675447322.203284125432.399910377813.9042612614
30.01198812023170.01882351580490.04078127600180.01779088512830.03891058329250.104935530059-0.1143993033670.02494903119410.158483832297-0.01541835932920.00247843219052-0.30690044846-0.1869630106590.234688311403-0.6175559911440.0994598205196-0.08955167255-0.03044136146320.2961807343570.06222345719880.34409198028512.619247169630.258266948221.3631579343
40.118135939003-0.0544387063710.1004563052410.0631690466959-0.1187940762860.2055278087460.08403924375550.0893313006736-0.0924219963378-0.06391284116290.03695846309880.07658425269750.135482701818-0.005176025424851.321952744290.0923872154042-0.0828817966274-0.06337327280130.123063974202-0.12076499347-0.183191978267-0.28652970054542.106688398514.6957205411
50.37309520194-0.008046814403140.140074958860.00413521221081-0.003642736008820.06408103383070.0281872132730.2164245707150.15041592725-0.1484245241170.0249733759207-0.0990786986945-0.2868647018080.154208541040.3243900073820.413476546255-0.2741142400750.1926209369120.06571398263550.02266221927590.17943084935211.314224668843.40045054418.44783994149
60.0316625004733-0.01372191162010.02117076588140.03188972032380.01171231949960.0232550115837-0.1438755001560.169858848884-0.0554056080174-0.1862738741090.1316284827370.248153881094-0.0510859348957-0.3288114262010.0002907993493290.823107987316-0.0049298209305-0.0765450951580.4552619496490.0324098874260.8010754189233.9925168224669.25320209116.93341810207
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 50 through 84 )50 - 841 - 35
22chain 'A' and (resid 85 through 109 )85 - 10936 - 60
33chain 'A' and (resid 110 through 156 )110 - 15661 - 101
44chain 'A' and (resid 157 through 241 )157 - 241102 - 186
55chain 'A' and (resid 242 through 317 )242 - 317187 - 262
66chain 'A' and (resid 318 through 352 )318 - 352263 - 294

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