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- PDB-7akw: Crystal structure of the viral rhodopsins chimera O1O2 -

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Basic information

Entry
Database: PDB / ID: 7akw
TitleCrystal structure of the viral rhodopsins chimera O1O2
Componentschimera of viral rhodopsins OLPVR1 and OLPVRII
KeywordsMEMBRANE PROTEIN / rhodopsin / viral rhodopsin / giant virus / ion channel / retinal / ion transport / light-gated channel / channelrhodopsin / bacteriorhodopsin
Function / homology
Function and homology information


photoreceptor activity / phototransduction / monoatomic ion channel activity / membrane
Similarity search - Function
Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein
Similarity search - Domain/homology
EICOSANE / RETINAL / Uncharacterized protein
Similarity search - Component
Biological speciesOrganic Lake phycodnavirus (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsKovalev, K. / Zabelskii, D. / Alekseev, A. / Astashkin, R. / Gordeliy, V.
Funding support France, Russian Federation, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-19-CE11-0026 France
Russian Foundation for Basic Research21-54-12020 Russian Federation
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)ANR-10-INBS-05-02 France
CitationJournal: Nat Commun / Year: 2020
Title: Viral rhodopsins 1 are an unique family of light-gated cation channels.
Authors: Zabelskii, D. / Alekseev, A. / Kovalev, K. / Rankovic, V. / Balandin, T. / Soloviov, D. / Bratanov, D. / Savelyeva, E. / Podolyak, E. / Volkov, D. / Vaganova, S. / Astashkin, R. / Chizhov, I. ...Authors: Zabelskii, D. / Alekseev, A. / Kovalev, K. / Rankovic, V. / Balandin, T. / Soloviov, D. / Bratanov, D. / Savelyeva, E. / Podolyak, E. / Volkov, D. / Vaganova, S. / Astashkin, R. / Chizhov, I. / Yutin, N. / Rulev, M. / Popov, A. / Eria-Oliveira, A.S. / Rokitskaya, T. / Mager, T. / Antonenko, Y. / Rosselli, R. / Armeev, G. / Shaitan, K. / Vivaudou, M. / Buldt, G. / Rogachev, A. / Rodriguez-Valera, F. / Kirpichnikov, M. / Moser, T. / Offenhausser, A. / Willbold, D. / Koonin, E. / Bamberg, E. / Gordeliy, V.
History
DepositionOct 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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: chimera of viral rhodopsins OLPVR1 and OLPVRII
B: chimera of viral rhodopsins OLPVR1 and OLPVRII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8066
Polymers53,6722
Non-polymers1,1344
Water93752
1
A: chimera of viral rhodopsins OLPVR1 and OLPVRII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4033
Polymers26,8361
Non-polymers5672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: chimera of viral rhodopsins OLPVR1 and OLPVRII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4033
Polymers26,8361
Non-polymers5672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.405, 103.396, 111.381
Angle α, β, γ (deg.)90.000, 90.320, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein chimera of viral rhodopsins OLPVR1 and OLPVRII


Mass: 26835.877 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Organic Lake phycodnavirus (environmental samples)
Gene: 162281038 / Production host: Escherichia coli (E. coli) / References: UniProt: F2Y337
#2: Chemical ChemComp-LFA / EICOSANE / LIPID FRAGMENT / Icosane


Mass: 282.547 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H42
#3: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C20H28O
Source: (gene. exp.) Organic Lake phycodnavirus (environmental samples)
Production host: Escherichia coli (E. coli) / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 4.6 / Details: 1.8 M Na2HPO4/KH2PO4 (pH 4.6)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.96→41.33 Å / Num. obs: 36098 / % possible obs: 99.5 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.032 / Rrim(I) all: 0.061 / Net I/σ(I): 12.2 / Num. measured all: 126043
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.4 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.96-21.191839324480.5080.7421.4070.995.4
8.97-41.330.02112933820.9990.0130.02551.397.8

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6sqg

6sqg


Resolution: 1.96→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.267 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2458 1776 4.9 %RANDOM
Rwork0.202 ---
obs0.2041 34293 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.78 Å2 / Biso mean: 41.622 Å2 / Biso min: 25.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å22.21 Å2
2---1.17 Å20 Å2
3---2.11 Å2
Refinement stepCycle: final / Resolution: 1.96→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3777 0 32 52 3861
Biso mean--58.11 42.54 -
Num. residues----444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0133961
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173799
X-RAY DIFFRACTIONr_angle_refined_deg1.0531.645372
X-RAY DIFFRACTIONr_angle_other_deg1.1571.5728623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8815450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.76822.873181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.55515656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.803158
X-RAY DIFFRACTIONr_chiral_restr0.0470.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024242
X-RAY DIFFRACTIONr_gen_planes_other00.02940
LS refinement shellResolution: 1.96→2.007 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.326 115 -
Rwork-2434 -
obs--95.58 %

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