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- PDB-9in7: True-atomic resolution crystal structure of the closed state of t... -

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Basic information

Entry
Database: PDB / ID: 9in7
TitleTrue-atomic resolution crystal structure of the closed state of the viral channelrhodopsin OLPVR1
ComponentsViral rhodopsin OLPVR1
KeywordsMEMBRANE PROTEIN / rhodopsin / ChR2 / open state / open channel / ChRMine / cation-conducting ChR
Function / homology
Function and homology information


monoatomic ion channel activity / photoreceptor activity / phototransduction / membrane
Similarity search - Function
Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein
Similarity search - Domain/homology
(2S)-2,3-dihydroxypropyl (9Z)-hexadec-9-enoate / EICOSANE / (2R)-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: 1.13 Å
AuthorsBukhdruker, S. / Zabelskii, D. / Astashkin, R. / Gordeliy, V.
Funding support France, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-15-CE11-0029-02 France
Agence Nationale de la Recherche (ANR)ANR-19-CE11-0026 France
Agence Nationale de la Recherche (ANR)ANR-11-LABX-0015-01 France
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2025
Title: Ion-conducting and gating molecular mechanisms of channelrhodopsin revealed by true-atomic-resolution structures of open and closed states.
Authors: Zabelskii, D. / Bukhdruker, S. / Bukhalovich, S. / Tsybrov, F. / Lamm, G.H.U. / Astashkin, R. / Doroginin, D. / Matveev, G. / Sudarev, V. / Kuzmin, A. / Zinovev, E. / Vlasova, A. / Ryzhykau, ...Authors: Zabelskii, D. / Bukhdruker, S. / Bukhalovich, S. / Tsybrov, F. / Lamm, G.H.U. / Astashkin, R. / Doroginin, D. / Matveev, G. / Sudarev, V. / Kuzmin, A. / Zinovev, E. / Vlasova, A. / Ryzhykau, Y. / Ilyinsky, N. / Gushchin, I. / Bourenkov, G. / Alekseev, A. / Round, A. / Wachtveitl, J. / Bamberg, E. / Gordeliy, V.
History
DepositionJul 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2025Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Viral rhodopsin OLPVR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,00423
Polymers28,1271
Non-polymers5,87722
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.498, 114.948, 53.171
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-451-

HOH

21A-536-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Viral rhodopsin OLPVR1


Mass: 28127.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Organic Lake phycodnavirus (environmental samples)
Gene: 162281038 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: F2Y337

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Non-polymers , 7 types, 168 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-97N / (2S)-2,3-dihydroxypropyl (9Z)-hexadec-9-enoate


Mass: 328.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H36O4
#5: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H40O4
#6: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C20H42
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 52.96 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8 / Details: 100 mM Tris, 900 mM NaCl, and 24% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Sep 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.13→33.48 Å / Num. obs: 78116 / % possible obs: 94.3 % / Redundancy: 4.8 % / Biso Wilson estimate: 17.17 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.022 / Net I/σ(I): 12.1
Reflection shellResolution: 1.13→1.23 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3905 / CC1/2: 0.22 / Rpim(I) all: 1.066 / % possible all: 70.8

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Processing

Software
NameVersionClassification
MxCuBE3data collection
XDSdata reduction
STARANISOdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AKY

7aky


Resolution: 1.13→33.48 Å / SU ML: 0.1208 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.0782
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1838 3898 4.99 %
Rwork0.1513 74147 -
obs0.153 78045 72.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.02 Å2
Refinement stepCycle: LAST / Resolution: 1.13→33.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1914 0 257 146 2317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00872467
X-RAY DIFFRACTIONf_angle_d1.06163292
X-RAY DIFFRACTIONf_chiral_restr0.0856340
X-RAY DIFFRACTIONf_plane_restr0.0078386
X-RAY DIFFRACTIONf_dihedral_angle_d15.8221961
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.140.256520.295131X-RAY DIFFRACTION0.88
1.14-1.160.178460.332120X-RAY DIFFRACTION3.41
1.16-1.170.4533150.3387297X-RAY DIFFRACTION8.26
1.17-1.190.3006330.3236606X-RAY DIFFRACTION16.89
1.19-1.210.335470.3078906X-RAY DIFFRACTION25.16
1.21-1.220.363690.30761296X-RAY DIFFRACTION35.66
1.22-1.240.2912820.30781568X-RAY DIFFRACTION43.59
1.24-1.260.3094960.29471821X-RAY DIFFRACTION49.86
1.26-1.280.31551110.29052095X-RAY DIFFRACTION58.36
1.28-1.310.31371280.28472438X-RAY DIFFRACTION67.07
1.31-1.330.28371440.26182717X-RAY DIFFRACTION75.03
1.33-1.360.29071570.24872960X-RAY DIFFRACTION82.07
1.36-1.390.29751670.23463151X-RAY DIFFRACTION87.18
1.39-1.420.28691700.21493322X-RAY DIFFRACTION90.98
1.42-1.460.25342050.19193427X-RAY DIFFRACTION95.2
1.46-1.50.2471980.16533578X-RAY DIFFRACTION98.51
1.5-1.540.23011920.14893606X-RAY DIFFRACTION99.01
1.54-1.590.17592010.14153585X-RAY DIFFRACTION99.27
1.59-1.650.1891930.13383630X-RAY DIFFRACTION99.27
1.65-1.710.18661640.12813666X-RAY DIFFRACTION99.35
1.71-1.790.16621650.12933657X-RAY DIFFRACTION99.32
1.79-1.890.16951800.11623647X-RAY DIFFRACTION99.4
1.89-20.15411950.11133641X-RAY DIFFRACTION99.2
2-2.160.13431790.11033664X-RAY DIFFRACTION98.97
2.16-2.380.14381890.11643675X-RAY DIFFRACTION98.95
2.38-2.720.15972110.12973635X-RAY DIFFRACTION97.89
2.72-3.430.15591830.14663650X-RAY DIFFRACTION96.89
3.43-33.480.19952160.17473758X-RAY DIFFRACTION95.6

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