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- PDB-7c86: Time-resolved serial femtosecond crystallography reveals early st... -

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Basic information

Entry
Database: PDB / ID: 7c86
TitleTime-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: Dark state structure
ComponentsSensory opsin A,Channelrhodopsin (ChR) chimera between ChR1 & ChR2
KeywordsMEMBRANE PROTEIN / Channelrhodopsin / Rhodopsin
Function / homology
Function and homology information


photoreceptor activity / phototransduction / metal ion binding / 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 / Sensory opsin A
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsOda, K. / Nomura, T. / Nakane, T. / Yamashita, K. / Inoue, K. / Ito, S. / Vierock, J. / Hirata, K. / Maturana, A.D. / Katayama, K. ...Oda, K. / Nomura, T. / Nakane, T. / Yamashita, K. / Inoue, K. / Ito, S. / Vierock, J. / Hirata, K. / Maturana, A.D. / Katayama, K. / Ikuta, T. / Ishigami, I. / Izume, T. / Umeda, R. / Eguma, R. / Oishi, S. / Kasuya, G. / Kato, T. / Kusakizako, T. / Shihoya, W. / Shimada, H. / Takatsuji, T. / Takemoto, M. / Taniguchi, R. / Tomita, A. / Nakamura, R. / Fukuda, M. / Miyauchi, H. / Lee, Y. / Nango, E. / Tanaka, R. / Tanaka, T. / Sugahara, M. / Kimura, T. / Shimamura, T. / Fujiwara, T. / Yamanaka, Y. / Owada, S. / Joti, Y. / Tono, K. / Ishitani, R. / Hayashi, S. / Kandori, H. / Hegemann, P. / Iwata, S. / Kubo, M. / Nishizawa, T. / Nureki, O.
CitationJournal: Elife / Year: 2021
Title: Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin.
Authors: Oda, K. / Nomura, T. / Nakane, T. / Yamashita, K. / Inoue, K. / Ito, S. / Vierock, J. / Hirata, K. / Maturana, A.D. / Katayama, K. / Ikuta, T. / Ishigami, I. / Izume, T. / Umeda, R. / Eguma, ...Authors: Oda, K. / Nomura, T. / Nakane, T. / Yamashita, K. / Inoue, K. / Ito, S. / Vierock, J. / Hirata, K. / Maturana, A.D. / Katayama, K. / Ikuta, T. / Ishigami, I. / Izume, T. / Umeda, R. / Eguma, R. / Oishi, S. / Kasuya, G. / Kato, T. / Kusakizako, T. / Shihoya, W. / Shimada, H. / Takatsuji, T. / Takemoto, M. / Taniguchi, R. / Tomita, A. / Nakamura, R. / Fukuda, M. / Miyauchi, H. / Lee, Y. / Nango, E. / Tanaka, R. / Tanaka, T. / Sugahara, M. / Kimura, T. / Shimamura, T. / Fujiwara, T. / Yamanaka, Y. / Owada, S. / Joti, Y. / Tono, K. / Ishitani, R. / Hayashi, S. / Kandori, H. / Hegemann, P. / Iwata, S. / Kubo, M. / Nishizawa, T. / Nureki, O.
History
DepositionMay 28, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sensory opsin A,Channelrhodopsin (ChR) chimera between ChR1 & ChR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,61012
Polymers39,6931
Non-polymers3,91811
Water68538
1
A: Sensory opsin A,Channelrhodopsin (ChR) chimera between ChR1 & ChR2
hetero molecules

A: Sensory opsin A,Channelrhodopsin (ChR) chimera between ChR1 & ChR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,22124
Polymers79,3852
Non-polymers7,83522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area8090 Å2
ΔGint-52 kcal/mol
Surface area26920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.800, 142.200, 94.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Sensory opsin A,Channelrhodopsin (ChR) chimera between ChR1 & ChR2


Mass: 39692.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CSOA / Plasmid: pFastBac / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8L435
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.62 Å3/Da / Density % sol: 53.07 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.9
Details: 100 mM MES, pH 6.9, 100 mM Na formate, and 30% PEG500DME

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.77 Å
DetectorType: MPCCD / Detector: CCD / Date: Oct 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 2.3→47.35 Å / Num. obs: 18961 / % possible obs: 100 % / Redundancy: 561.2 % / CC1/2: 0.9962 / R split: 0.061 / Net I/σ(I): 9.64
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2R split
6.238-48.781550.719.4610410.99640.0448
4.953-6.2381036.618.389900.99290.0538
4.327-4.953906.420.059510.99340.05
3.932-4.327809.618.519660.99060.056
3.651-3.932686.616.679440.98840.0612
3.435-3.651599.914.89550.99180.0631
3.264-3.435595.713.059500.98860.0734
3.121-3.264579.811.769380.98690.0764
3.001-3.121556.510.589460.98810.0876
2.898-3.001529.98.659400.98510.1038
2.807-2.898502.87.589450.98550.1131
2.727-2.807469.66.39450.97690.1444
2.655-2.727436.65.359210.97160.174
2.59-2.6553964.669210.96430.1982
2.532-2.59344.13.579690.950.2654
2.478-2.532292.83.219150.93280.3086
2.428-2.478246.82.499330.84130.4179
2.382-2.428207.82.039380.8240.4923
2.34-2.382172.81.689380.82810.5783
2.3-2.34138.51.559150.84210.6049
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
PDB_EXTRACT3.25data extraction
CrystFEL0.6.3data reduction
CrystFEL0.6.3data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UG9

3ug9


Resolution: 2.3→15 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.45 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.242 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2322 901 4.8 %RANDOM
Rwork0.182 ---
obs0.1843 17940 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 171.96 Å2 / Biso mean: 67.069 Å2 / Biso min: 35.47 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å2-0 Å2-0 Å2
2---5.49 Å20 Å2
3---3.9 Å2
Refinement stepCycle: final / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2317 0 174 38 2529
Biso mean--113.29 66.42 -
Num. residues----296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132545
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172439
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.6483426
X-RAY DIFFRACTIONr_angle_other_deg1.3141.5735598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8275293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58721.478115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.24115371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.455157
X-RAY DIFFRACTIONr_chiral_restr0.0690.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022779
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02585
LS refinement shellResolution: 2.3→2.358 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 66 -
Rwork0.298 1270 -
all-1336 -
obs--99.63 %

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