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- PDB-9h20: Continuous dark state structure of Sensory Rhodopsin II solved by... -

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Basic information

Entry
Database: PDB / ID: 9h20
TitleContinuous dark state structure of Sensory Rhodopsin II solved by serial millisecond crystallography
ComponentsSensory rhodopsin-2
KeywordsSIGNALING PROTEIN / SRII / serial millisecond crystallography / sensory rhodopsin / sensory rhodopsin II / SMX / SSX
Function / homology
Function and homology information


monoatomic ion channel activity / photoreceptor activity / phototransduction / plasma membrane
Similarity search - Function
Bacterial rhodopsins retinal binding site. / Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein
Similarity search - Domain/homology
Chem-MPG / RETINAL / Sensory rhodopsin-2
Similarity search - Component
Biological speciesNatronomonas pharaonis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsOrtolani, G. / Bosman, R. / Branden, G. / Neutze, R.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission637295European Union
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis for the prolonged photocycle of sensory rhodopsin II revealed by serial synchrotron crystallography.
Authors: Bosman, R. / Ortolani, G. / Ghosh, S. / James, D. / Norder, P. / Hammarin, G. / Ulfarsdottir, T.B. / Ostojic, L. / Weinert, T. / Dworkowski, F. / Tomizaki, T. / Standfuss, J. / Branden, G. / Neutze, R.
History
DepositionOct 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release
SupersessionMay 28, 2025ID: 7PNC
Revision 1.1May 28, 2025Group: Advisory / Category: pdbx_database_PDB_obs_spr

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sensory rhodopsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,46417
Polymers26,6661
Non-polymers4,79816
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint17 kcal/mol
Surface area11380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.750, 131.700, 51.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

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Components

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Protein / Sugars , 2 types, 9 molecules A

#1: Protein Sensory rhodopsin-2 / Sensory rhodopsin II / SR-II


Mass: 26666.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sensory rhodopsin II, transmembrane protein / Source: (gene. exp.) Natronomonas pharaonis (archaea) / Gene: sop2, sopII / Production host: Escherichia coli (E. coli) / References: UniProt: P42196
#4: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C14H28O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 41 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-MPG / [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate


Mass: 356.540 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H40O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.83 Å3/Da / Density % sol: 56.47 %
Crystal growTemperature: 296 K / Method: lipidic cubic phase
Details: CaCl2 150mM, Glycine 100mM, 38%(v/v) PEG 400, pH 7.5

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Data collection

DiffractionMean temperature: 296 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0000342 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0000342 Å / Relative weight: 1
ReflectionResolution: 2.2→39.44 Å / Num. obs: 18087 / % possible obs: 100 % / Redundancy: 242.5 % / Biso Wilson estimate: 34.27 Å2 / CC1/2: 0.991 / Net I/σ(I): 5.6
Reflection shellResolution: 2.2→39.44 Å / Num. unique obs: 18087 / CC1/2: 0.991

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→39.44 Å / SU ML: 0.2328 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.9155
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2184 781 4.97 %
Rwork0.2069 14948 -
obs0.2075 15729 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.28 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1603 0 315 33 1951
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00791952
X-RAY DIFFRACTIONf_angle_d1.09882613
X-RAY DIFFRACTIONf_chiral_restr0.5504323
X-RAY DIFFRACTIONf_plane_restr0.0039283
X-RAY DIFFRACTIONf_dihedral_angle_d19.5435372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.340.26241270.27042415X-RAY DIFFRACTION99.88
2.34-2.520.27981190.23682476X-RAY DIFFRACTION99.92
2.52-2.770.23481310.21712466X-RAY DIFFRACTION99.88
2.77-3.170.20971290.20382481X-RAY DIFFRACTION100
3.17-40.19531260.18742508X-RAY DIFFRACTION100
4-39.440.21061490.19812602X-RAY DIFFRACTION99.85

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