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- PDB-8r0n: Cryo-EM structure of the microbial rhodopsin CryoR1 at pH 10.5 in... -

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Basic information

Entry
Database: PDB / ID: 8r0n
TitleCryo-EM structure of the microbial rhodopsin CryoR1 at pH 10.5 in detergent in the ground state
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: 2.7 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: Sci Adv / Year: 2025
Title: CryoRhodopsins: A comprehensive characterization of a group of microbial rhodopsins from cold environments.
Authors: Gerrit H U Lamm / Egor Marin / Alexey Alekseev / Anna V Schellbach / Artem Stetsenko / Jose Manuel Haro-Moreno / Gleb Bourenkov / Valentin Borshchevskiy / Marvin Asido / Michael Agthe / ...Authors: Gerrit H U Lamm / Egor Marin / Alexey Alekseev / Anna V Schellbach / Artem Stetsenko / Jose Manuel Haro-Moreno / Gleb Bourenkov / Valentin Borshchevskiy / Marvin Asido / Michael Agthe / Sylvain Engilberge / Samuel L Rose / Nicolas Caramello / Antoine Royant / Thomas R Schneider / Alex Bateman / Thomas Mager / Tobias Moser / Francisco Rodriguez-Valera / Josef Wachtveitl / Albert Guskov / Kirill Kovalev /
Abstract: Microbial rhodopsins are omnipresent on Earth; however, the vast majority of them remain uncharacterized. Here, we describe a rhodopsin group found in microorganisms from cold environments, such as ...Microbial rhodopsins are omnipresent on Earth; however, the vast majority of them remain uncharacterized. Here, we describe a rhodopsin group found in microorganisms from cold environments, such as glaciers, denoted as CryoRhodopsins (CryoRs). A distinguishing feature of the group is the presence of a buried arginine residue close to the cytoplasmic face. Combining single-particle cryo-electron microscopy and x-ray crystallography with rhodopsin activation by light, we demonstrate that the arginine stabilizes an ultraviolet (UV)-absorbing intermediate of an extremely slow CryoRhodopsin photocycle. Together with extensive spectroscopic characterization, our investigations on CryoR1 and CryoR2 proteins reveal mechanisms of photoswitching in the identified group. Our data suggest that CryoRs are sensors for UV irradiation and are also capable of inward proton translocation modulated by UV light.
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
Revision 1.1Jul 16, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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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)180,29316
Polymers176,0355
Non-polymers4,25811
Water1,40578
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-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: Chemical ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C20H42
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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 10.5, 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: 10.5
SpecimenConc.: 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: 1200 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
12cryoSPARC4.1.2classification
13cryoSPARC4.1.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 200653 / Symmetry type: POINT
RefinementResolution: 2.7→101.16 Å / Cor.coef. Fo:Fc: 0.598 / SU B: 10.55 / SU ML: 0.199 / ESU R: 0.537
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.44495 --
obs0.44495 98421 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 46.352 Å2
Refinement stepCycle: 1 / Total: 10921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0090.01211102
ELECTRON MICROSCOPYr_bond_other_d00.01610894
ELECTRON MICROSCOPYr_angle_refined_deg1.3011.63115179
ELECTRON MICROSCOPYr_angle_other_deg0.4581.55624967
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.02951410
ELECTRON MICROSCOPYr_dihedral_angle_2_deg8.687597
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.273101659
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0650.21910
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.0212616
ELECTRON MICROSCOPYr_gen_planes_other0.0020.022470
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_it6.2164.2565655
ELECTRON MICROSCOPYr_mcbond_other6.2164.2565655
ELECTRON MICROSCOPYr_mcangle_it9.537.6427060
ELECTRON MICROSCOPYr_mcangle_other9.537.6437061
ELECTRON MICROSCOPYr_scbond_it7.2495.0165447
ELECTRON MICROSCOPYr_scbond_other7.2495.0155447
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other11.8038.8788120
ELECTRON MICROSCOPYr_long_range_B_refined14.49540.913295
ELECTRON MICROSCOPYr_long_range_B_other14.50140.9113286
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork2.544 7349 -
obs--100 %

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