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- PDB-5zih: Crystal structure of the red light-activated channelrhodopsin Chr... -

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Basic information

Entry
Database: PDB / ID: 5zih
TitleCrystal structure of the red light-activated channelrhodopsin Chrimson.
ComponentsSensory opsin A,Chrimson
KeywordsMEMBRANE PROTEIN / rhodopsin / ion channel
Function / homologyBacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / endoplasmic reticulum / metal ion binding / plasma membrane / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Sensory opsin A
Function and homology information
Biological speciesChlamydomonas reinhardtii (plant)
Chlamydomonas noctigama (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsOda, K. / Vierock, J. / Oishi, S. / Taniguchi, R. / Yamashita, K. / Nishizawa, T. / Hegemann, P. / Nureki, O.
Funding support Japan, 2items
OrganizationGrant numberCountry
MEXT16H06294 Japan
JSTJPMJPR14L8 Japan
CitationJournal: Nat Commun / Year: 2018
Title: Crystal structure of the red light-activated channelrhodopsin Chrimson.
Authors: Oda, K. / Vierock, J. / Oishi, S. / Rodriguez-Rozada, S. / Taniguchi, R. / Yamashita, K. / Wiegert, J.S. / Nishizawa, T. / Hegemann, P. / Nureki, O.
History
DepositionMar 15, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sensory opsin A,Chrimson
B: Sensory opsin A,Chrimson
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,69321
Polymers77,9182
Non-polymers6,77419
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-61 kcal/mol
Surface area25110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.990, 81.440, 170.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sensory opsin A,Chrimson


Mass: 38959.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Chrimson with substituted N-terminal CrChR1 sequence
Source: (gene. exp.) Chlamydomonas reinhardtii (plant), (gene. exp.) Chlamydomonas noctigama (plant)
Gene: CSOA / Plasmid: pFastBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8L435
#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C21H40O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.73 Å3/Da / Density % sol: 54.95 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 7 / Details: PEG500DME, Na citrate, Na malonate, sarcosine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 30180 / % possible obs: 100 % / Redundancy: 9.3 % / Biso Wilson estimate: 24.96 Å2 / CC1/2: 0.98 / Rrim(I) all: 0.144 / Χ2: 1.237 / Net I/σ(I): 13.8 / Num. measured all: 276798 / Scaling rejects: 214
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 1.7 / Num. measured obs: 41376 / Num. possible: 4768 / Num. unique obs: 4767 / CC1/2: 0.595 / Rrim(I) all: 0.591 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UG9

3ug9


Resolution: 2.6→48.818 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2788 2671 9.98 %
Rwork0.2282 24080 -
obs0.2333 26751 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.21 Å2 / Biso mean: 38.6213 Å2 / Biso min: 3.56 Å2
Refinement stepCycle: final / Resolution: 2.6→48.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4410 0 374 37 4821
Biso mean--41.9 25.08 -
Num. residues----564
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6001-2.64730.36861380.31441250138899
2.6473-2.69830.34551370.304412351372100
2.6983-2.75330.34791400.276412701410100
2.7533-2.81320.3471380.273712401378100
2.8132-2.87860.2951390.28412411380100
2.8786-2.95060.32621380.262312561394100
2.9506-3.03040.28091370.25311238137599
3.0304-3.11950.30941390.233912531392100
3.1195-3.22020.28191400.228112551395100
3.2202-3.33530.29321400.22681249138999
3.3353-3.46880.27011400.234112631403100
3.4688-3.62660.26461420.220212751417100
3.6266-3.81770.2481390.20612581397100
3.8177-4.05680.25011400.192712771417100
4.0568-4.36990.24861430.187812691412100
4.3699-4.80930.25061400.18612761416100
4.8093-5.50440.2371460.211113001446100
5.5044-6.93170.29291440.228113061450100
6.9317-48.82650.26071510.21861369152098

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