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- PDB-8r0l: Cryo-EM structure of the microbial rhodopsin CryoR1 at pH 8.0 in ... -

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Basic information

Entry
Database: PDB / ID: 8r0l
TitleCryo-EM structure of the microbial rhodopsin CryoR1 at pH 8.0 in nanodisc
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: 2.43 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)183,10830
Polymers176,0355
Non-polymers7,07325
Water4,324240
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: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C20H42
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: in nanodisc, pH 8.0, ground state of CryoR1 / 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.: 2.7 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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k 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
13cryoSPARC4.1.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 2.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 218132 / Symmetry type: POINT
RefinementResolution: 2.43→101.99 Å / Cor.coef. Fo:Fc: 0.601 / SU B: 7.584 / SU ML: 0.153 / ESU R: 0.403
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.47021 --
obs0.47021 134811 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 42.753 Å2
Refinement stepCycle: 1 / Total: 11200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.01211195
ELECTRON MICROSCOPYr_bond_other_d00.01611312
ELECTRON MICROSCOPYr_angle_refined_deg1.3931.63415205
ELECTRON MICROSCOPYr_angle_other_deg0.4651.55625887
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.71951405
ELECTRON MICROSCOPYr_dihedral_angle_2_deg11.6745109
ELECTRON MICROSCOPYr_dihedral_angle_3_deg18.087101675
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0720.21855
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.0212743
ELECTRON MICROSCOPYr_gen_planes_other0.0020.022535
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_it4.83.8245635
ELECTRON MICROSCOPYr_mcbond_other4.83.8245635
ELECTRON MICROSCOPYr_mcangle_it7.4026.8767035
ELECTRON MICROSCOPYr_mcangle_other7.4026.8777036
ELECTRON MICROSCOPYr_scbond_it5.6894.5865560
ELECTRON MICROSCOPYr_scbond_other5.6884.5875561
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other9.3588.0658171
ELECTRON MICROSCOPYr_long_range_B_refined11.90436.613278
ELECTRON MICROSCOPYr_long_range_B_other11.89436.613248
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.43→2.493 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork3.177 9951 -
obs--100 %

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