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- PDB-9in8: True-atomic resolution crystal structure of the open state of the... -

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Basic information

Entry
Database: PDB / ID: 9in8
TitleTrue-atomic resolution crystal structure of the open 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: 1.34 Å
AuthorsBukhdruker, S. / Zabelskii, D. / Astashkin, R. / Bourenkov, G. / Gordeliy, V.
Funding support France, 2items
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
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

Downloads & links

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Assembly

Deposited unit
A: Viral rhodopsin OLPVR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,72222
Polymers28,1271
Non-polymers5,59421
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.427, 115.029, 53.337
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-314-

GOL

21A-449-

HOH

31A-545-

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, 172 molecules

#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / 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.: 9 / 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.: 151 / 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: 2.74 Å3/Da / Density % sol: 55.1 %
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: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Mar 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.34→43.05 Å / Num. obs: 47593 / % possible obs: 93.8 % / Redundancy: 13.1 % / Biso Wilson estimate: 20.81 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.024 / Net I/σ(I): 16.1
Reflection shellResolution: 1.34→1.46 Å / Redundancy: 12.6 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2380 / CC1/2: 0.175 / Rpim(I) all: 1.331 / % possible all: 57.8

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Processing

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

7aky


Resolution: 1.34→39.11 Å / SU ML: 0.1612 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.4736
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.212 2346 4.94 %
Rwork0.1838 45166 -
obs0.1853 47512 72.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.24 Å2
Refinement stepCycle: LAST / Resolution: 1.34→39.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1908 0 248 151 2307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00792958
X-RAY DIFFRACTIONf_angle_d0.90193980
X-RAY DIFFRACTIONf_chiral_restr0.0757413
X-RAY DIFFRACTIONf_plane_restr0.0058475
X-RAY DIFFRACTIONf_dihedral_angle_d15.82611135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.370.457430.351105X-RAY DIFFRACTION2.89
1.37-1.40.343120.3761286X-RAY DIFFRACTION7.97
1.4-1.430.3743300.3655692X-RAY DIFFRACTION19.18
1.43-1.460.3733790.31251169X-RAY DIFFRACTION32.91
1.46-1.50.3811940.31541831X-RAY DIFFRACTION50.64
1.5-1.550.31211240.30122330X-RAY DIFFRACTION64.66
1.55-1.60.30191480.28852743X-RAY DIFFRACTION76.26
1.6-1.650.32781610.26953103X-RAY DIFFRACTION85.47
1.65-1.720.28411650.25983419X-RAY DIFFRACTION93.9
1.72-1.80.26611550.23193627X-RAY DIFFRACTION99.76
1.8-1.890.2551830.20043629X-RAY DIFFRACTION99.82
1.89-2.010.21921970.17313637X-RAY DIFFRACTION99.84
2.01-2.170.17281780.14963652X-RAY DIFFRACTION99.95
2.17-2.390.17151890.15013669X-RAY DIFFRACTION99.87
2.39-2.730.17272120.15183680X-RAY DIFFRACTION99.97
2.73-3.440.19411880.16223718X-RAY DIFFRACTION99.87
3.44-39.110.21282280.18813876X-RAY DIFFRACTION99.64
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.600499134498-0.06663934848530.0149369747681.164100498260.5105685410730.2028077556490.05179425477220.05865828801880.0526808967467-0.07795467643660.0186077396007-0.104626214174-0.2661989223550.159091256146-0.0002453122131890.150969197147-0.0486407814408-0.007061409899670.1965849400250.002634098960010.2126106209332.2178650761224.791950603-2.49818443832
20.00824067966579-0.0163201565455-0.01625519476560.06523219800360.01825770696050.01445355006040.0336499421880.261347508233-0.0850746315213-0.181488941836-0.06433614337960.151141321020.06216113964430.1210754421410.003371437287350.547153390950.00524623266001-0.0423603781190.5298699883020.09584052013980.2752448480082.5409792788716.5486288429-22.8071621235
30.759640430885-0.202198898323-0.2507108996160.996561096699-0.0200798995951.079267013660.00719180759290.0157114855692-0.0148547734674-0.0357982113306-0.01490959689140.1009827628920.116903450766-0.1088375285957.37019274074E-50.1280780174310.00893636591097-0.02003482422290.127026205694-0.009951365736750.153246019225-10.067045506610.39800293320.0542884960051
40.150629167528-0.2650132559640.1555038913170.481227590746-0.2203343635950.1160349033290.0275605891341-0.0267688590322-0.0166779926525-0.06357136115180.0799879601929-0.086637069196-0.4460796612720.1321858953449.81760485163E-50.191793834184-0.0103561908242-0.01302269114120.202530488759-0.006430998911930.214841209299-5.8335015122825.63352193762.77481975722
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 63 )2 - 632 - 63
22chain 'A' and (resid 64 through 69 )64 - 6964 - 69
33chain 'A' and (resid 70 through 188 )70 - 18870 - 188
44chain 'A' and (resid 189 through 224 )189 - 224189 - 224

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