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- PDB-7e6y: Time-resolved serial femtosecond crystallography reveals early st... -

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Basic information

Entry
Database: PDB / ID: 7e6y
TitleTime-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 1 microsecond structure
ComponentsArchaeal-type opsin 1,Archaeal-type opsin 2
KeywordsMEMBRANE PROTEIN / Channelrhodopsin / Rhodopsin
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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.5 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
DepositionFeb 24, 2021Deposition 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 1.3Nov 20, 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: Archaeal-type opsin 1,Archaeal-type opsin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,61012
Polymers39,6931
Non-polymers3,91811
Water68538
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)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 area8200 Å2
ΔGint-52 kcal/mol
Surface area26490 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 Archaeal-type opsin 1,Archaeal-type opsin 2 / Channelopsin-1 / Chlamyopsin 4 light-gated ion channel / Retinal binding protein / Sensory opsin B


Mass: 39692.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant)
Gene: acop1, cop4, acop2, COP4, CSOB, CHLRE_02g085257v5, CHLREDRAFT_182032
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q93WP2, UniProt: Q8RUT8
#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 %
Description: This is a time-resolved study and two sets of structure factors are deposited: extrapolated and observed data. Data collection statistics is about the latter but we used the former for ...Description: This is a time-resolved study and two sets of structure factors are deposited: extrapolated and observed data. Data collection statistics is about the latter but we used the former for refinement, where some reflections were rejected.
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.9
Details: 100 mM MES, pH 6.9, 100 mM Na formate, and 30% PEG500DM

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
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: 2.4→39.41 Å / Num. obs: 16730 / % possible obs: 100 % / Redundancy: 131.1 % / CC1/2: 0.9873 / R split: 0.1 / Net I/σ(I): 6.15
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2R split
6.506-39.526344.413.219160.97890.0864
5.168-6.506232.412.328650.98320.0815
4.515-5.16820213.868600.98710.0741
4.103-4.515184.313.68470.98020.0756
3.81-4.103168.912.198460.98770.0795
3.584-3.81145.510.668340.98320.0893
3.405-3.584126.88.188300.98180.1101
3.257-3.405126.26.788310.97430.1422
3.132-3.257122.85.718360.96960.1653
3.024-3.132120.14.888430.95870.1984
2.929-3.024116.13.858120.94350.2621
2.846-2.929111.53.088200.92220.3182
2.771-2.846106.42.668240.91390.3694
2.703-2.77198.62.228390.85790.4544
2.641-2.70390.21.878270.81550.5624
2.585-2.64180.21.558040.7840.6748
2.534-2.58568.31.348500.75170.7482
2.486-2.53457.11.238150.67660.882
2.441-2.48646.30.998230.54351.0745
2.4-2.44137.80.868080.43891.3251

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
CrystFEL0.6.3data reduction
CrystFEL0.6.3data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ug9

3ug9


Resolution: 2.5→14.96 Å / Cor.coef. Fo:Fc: 0.775 / Cor.coef. Fo:Fc free: 0.696 / SU B: 84.554 / SU ML: 1.692 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 3.559 / ESU R Free: 0.712 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.5148 542 4.9 %RANDOM
Rwork0.4448 ---
obs0.4485 10428 74.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 227.76 Å2 / Biso mean: 68.707 Å2 / Biso min: 11.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20 Å20 Å2
2---4.03 Å2-0 Å2
3---3.14 Å2
Refinement stepCycle: final / Resolution: 2.5→14.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2317 0 174 38 2529
Biso mean--73.57 45.06 -
Num. residues----296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132545
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172439
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.6483426
X-RAY DIFFRACTIONr_angle_other_deg1.2361.5735598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0494.993294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0221.579114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.41515371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.177157
X-RAY DIFFRACTIONr_chiral_restr0.0660.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022754
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02586
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.77 35 -
Rwork0.687 679 -
all-714 -
obs--66.98 %

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