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- PDB-6sqg: Crystal structure of viral rhodopsin OLPVRII -

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Basic information

Entry
Database: PDB / ID: 6sqg
TitleCrystal structure of viral rhodopsin OLPVRII
Components(viral rhodopsin ...) x 2
KeywordsMEMBRANE PROTEIN / rhodopsin / proton pump / ion transport / pentamer / viral rhodopsin
Function / homology
Function and homology information


: / photoreceptor activity / phototransduction / monoatomic ion channel activity / membrane => GO:0016020
Similarity search - Function
Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein
Similarity search - Domain/homology
EICOSANE / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Uncharacterized protein
Similarity search - Component
Biological speciesOrganic Lake phycodnavirus (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGushchin, I. / Kovalev, K. / Bratanov, D. / Polovinkin, V. / Astashkin, R. / Popov, A. / Bourenkov, G. / Gordeliy, V.
Funding support France, Russian Federation, 5items
OrganizationGrant numberCountry
French National Research AgencyANR-15-CE11-0029-02/FA 301/11-1 France
French National Research AgencyANR-10-INBS-05-02 France
Grenoble Alliance for Integrated Structural Cell BiologyANR-17-EURE-0003 France
Russian Foundation for Basic Research19-52-15017 Russian Federation
French National Research AgencyANR-14-CE09-0028 France
CitationJournal: Nat Commun / Year: 2019
Title: Unique structure and function of viral rhodopsins.
Authors: Bratanov, D. / Kovalev, K. / Machtens, J.P. / Astashkin, R. / Chizhov, I. / Soloviov, D. / Volkov, D. / Polovinkin, V. / Zabelskii, D. / Mager, T. / Gushchin, I. / Rokitskaya, T. / ...Authors: Bratanov, D. / Kovalev, K. / Machtens, J.P. / Astashkin, R. / Chizhov, I. / Soloviov, D. / Volkov, D. / Polovinkin, V. / Zabelskii, D. / Mager, T. / Gushchin, I. / Rokitskaya, T. / Antonenko, Y. / Alekseev, A. / Shevchenko, V. / Yutin, N. / Rosselli, R. / Baeken, C. / Borshchevskiy, V. / Bourenkov, G. / Popov, A. / Balandin, T. / Buldt, G. / Manstein, D.J. / Rodriguez-Valera, F. / Fahlke, C. / Bamberg, E. / Koonin, E. / Gordeliy, V.
History
DepositionSep 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 24, 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

Downloads & links

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Assembly

Deposited unit
A: viral rhodopsin OLPVRII
B: viral rhodopsin OLPVRII
C: viral rhodopsin OLPVRII
D: viral rhodopsin OLPVRII
E: viral rhodopsin OLPVRII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,82983
Polymers122,6335
Non-polymers22,19678
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43510 Å2
ΔGint244 kcal/mol
Surface area34640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.582, 99.699, 82.958
Angle α, β, γ (deg.)90.000, 117.170, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Viral rhodopsin ... , 2 types, 5 molecules ABCDE

#1: Protein
viral rhodopsin OLPVRII


Mass: 24312.383 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Organic Lake phycodnavirus (environmental samples)
Gene: 162286292 / Production host: Escherichia coli (E. coli) / References: UniProt: F2Y2Z0
#2: Protein viral rhodopsin OLPVRII


Mass: 25383.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Organic Lake phycodnavirus (environmental samples)
Gene: 162286292 / Production host: Escherichia coli (E. coli) / References: UniProt: F2Y2Z0

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Non-polymers , 4 types, 295 molecules

#3: Chemical...
ChemComp-LFA / EICOSANE / LIPID FRAGMENT / Icosane


Mass: 282.547 Da / Num. of mol.: 71 / Source method: obtained synthetically / Formula: C20H42
#4: Chemical
ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C20H28O
#5: Chemical ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.4 Å3/Da / Density % sol: 48.85 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: 0.2 M sodium malonate, pH 4.6 and 15% PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.9→41.37 Å / Num. obs: 89527 / % possible obs: 98.9 % / Redundancy: 4.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.043 / Rrim(I) all: 0.092 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.934.61.6132090945560.3820.8381.8221.198.7
10.23-41.374.10.02324325930.9990.0130.02742.395.9

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HYJ

4hyj


Resolution: 1.9→41.37 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.046 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.136
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2097 4363 4.9 %RANDOM
Rwork0.1706 ---
obs0.1726 85140 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 110.29 Å2 / Biso mean: 38.453 Å2 / Biso min: 20.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0 Å20.47 Å2
2---0.07 Å2-0 Å2
3----0.13 Å2
Refinement stepCycle: final / Resolution: 1.9→41.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8543 0 669 217 9429
Biso mean--62.37 48.5 -
Num. residues----1051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.029456
X-RAY DIFFRACTIONr_bond_other_d0.0040.029768
X-RAY DIFFRACTIONr_angle_refined_deg0.9871.99612581
X-RAY DIFFRACTIONr_angle_other_deg0.9313.00322030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.55851072
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94122.977383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.378151370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5421530
X-RAY DIFFRACTIONr_chiral_restr0.0640.21362
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029977
X-RAY DIFFRACTIONr_gen_planes_other00.022306
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 313 -
Rwork0.305 6233 -
all-6546 -
obs--98.36 %

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