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- PDB-8r0m: Cryo-EM structure of the microbial rhodopsin CryoR1 at pH 8.0 in ... -

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Basic information

Entry
Database: PDB / ID: 8r0m
TitleCryo-EM structure of the microbial rhodopsin CryoR1 at pH 8.0 in detergent
ComponentsRhodopsin
KeywordsMEMBRANE PROTEIN / rhodopsin / retinal / cryo-EM / light sensor
Function / homologyBacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / photoreceptor activity / phototransduction / membrane / EICOSANE / RETINAL / Rhodopsin
Function and homology information
Biological speciesCryobacterium levicorallinum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsKovalev, K. / Marin, E. / Stetsenko, A. / Guskov, A. / Lamm, G.H.U.
Funding support Germany, 1items
OrganizationGrant numberCountry
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND847543 Germany
CitationJournal: To Be Published
Title: CryoRhodopsins: a new clade of microbial rhodopsins from cold environments
Authors: Lamm, G.H.U. / Marin, E. / Schellbach, A.V. / Stetsenko, A. / Alekseev, A. / Bourenkov, G. / Agthe, M. / Engilberge, S. / Rose, S. / Caramello, N. / Royant, A. / Schneider, T.R. / Bateman, A. ...Authors: Lamm, G.H.U. / Marin, E. / Schellbach, A.V. / Stetsenko, A. / Alekseev, A. / Bourenkov, G. / Agthe, M. / Engilberge, S. / Rose, S. / Caramello, N. / Royant, A. / Schneider, T.R. / Bateman, A. / Wachtveitl, J. / Guskov, A. / Kovalev, K.
History
DepositionOct 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rhodopsin
B: Rhodopsin
C: Rhodopsin
D: Rhodopsin
E: Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,37834
Polymers176,0355
Non-polymers9,34429
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Rhodopsin


Mass: 35206.965 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryobacterium levicorallinum (bacteria)
Gene: E3O11_09160 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1I3DJQ0
#2: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#3: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C20H42
#4: Chemical
ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C20H28O
Source: (gene. exp.) Cryobacterium levicorallinum (bacteria)
Gene: E3O11_09160 / Production host: Escherichia coli (E. coli) / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Pentameric form of the microbial rhodopsin CryoR1 / Type: COMPLEX / Details: solubilized in DDM, pH 8.0 / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.182 MDa / Experimental value: NO
Source (natural)Organism: Cryobacterium levicorallinum (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Image recordingElectron dose: 53.1 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.1.2particle selection
4cryoSPARC4.1.2CTF correction
10cryoSPARC4.1.2initial Euler assignment
11cryoSPARC4.1.2final Euler assignment
12cryoSPARC4.1.2classification
13cryoSPARC4.1.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 333882 / Symmetry type: POINT
RefinementResolution: 2.87→100.16 Å / Cor.coef. Fo:Fc: 0.628 / SU B: 13.355 / SU ML: 0.238 / ESU R: 0.691
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.42063 --
obs0.42063 78255 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 36.467 Å2
Refinement stepCycle: 1 / Total: 11095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0090.01211281
ELECTRON MICROSCOPYr_bond_other_d00.01611280
ELECTRON MICROSCOPYr_angle_refined_deg1.5921.63615332
ELECTRON MICROSCOPYr_angle_other_deg0.5231.55425937
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.96451405
ELECTRON MICROSCOPYr_dihedral_angle_2_deg7.472590
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.761101678
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0680.21905
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.0212550
ELECTRON MICROSCOPYr_gen_planes_other0.0020.022440
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it4.2963.1315635
ELECTRON MICROSCOPYr_mcbond_other4.2953.1315635
ELECTRON MICROSCOPYr_mcangle_it6.9615.6157035
ELECTRON MICROSCOPYr_mcangle_other6.965.6157036
ELECTRON MICROSCOPYr_scbond_it5.7454.0155646
ELECTRON MICROSCOPYr_scbond_other5.7454.0165647
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other9.6826.9658298
ELECTRON MICROSCOPYr_long_range_B_refined12.16829.9913138
ELECTRON MICROSCOPYr_long_range_B_other12.16829.9913139
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.87→2.945 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork2.41 5702 -
obs--100 %

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