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- EMDB-18800: Cryo-EM structure of the microbial rhodopsin CryoR2 at pH 8.0 in ... -

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Basic information

Entry
Database: EMDB / ID: EMD-18800
TitleCryo-EM structure of the microbial rhodopsin CryoR2 at pH 8.0 in detergent
Map data
Sample
  • Complex: Pentameric form of the microbial rhodopsin CryoR2
    • Protein or peptide: microbial rhodopsin CryoR2
  • Ligand: EICOSANE
  • Ligand: RETINAL
  • Ligand: water
Keywordsrhodopsin / retinal / cryo-EM / light sensor / MEMBRANE PROTEIN
Biological speciesSubtercola endophyticus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.44 Å
AuthorsKovalev K / Marin E / Stetsenko A / Guskov A / Lamm GHU
Funding support Germany, 1 items
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, 2023-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18800.png

Downloads & links

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Map

FileDownload / File: emd_18800.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 384 pix.
= 321.024 Å		0.84 Å/pix.
x 384 pix.
= 321.024 Å		0.84 Å/pix.
x 384 pix.
= 321.024 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.836 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.316
Minimum - Maximum-1.8731314 - 2.8604486
Average (Standard dev.)0.000052084706 (±0.047685698)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 321.02402 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_18800_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18800_half_map_2.map
Projections & Slices
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Sample components

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Entire : Pentameric form of the microbial rhodopsin CryoR2

EntireName: Pentameric form of the microbial rhodopsin CryoR2
Components
  • Complex: Pentameric form of the microbial rhodopsin CryoR2
    • Protein or peptide: microbial rhodopsin CryoR2
  • Ligand: EICOSANE
  • Ligand: RETINAL
  • Ligand: water

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Supramolecule #1: Pentameric form of the microbial rhodopsin CryoR2

SupramoleculeName: Pentameric form of the microbial rhodopsin CryoR2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: solubilized in DDM, pH 8.0
Source (natural)Organism: Subtercola endophyticus (bacteria)
Molecular weightTheoretical: 182 KDa

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Macromolecule #1: microbial rhodopsin CryoR2

MacromoleculeName: microbial rhodopsin CryoR2 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Subtercola endophyticus (bacteria)
Molecular weightTheoretical: 34.973539 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRLTNVSVPW GATLSNAEHQ LIFYFLVVAA LAFVAGFIRT YITRNEVGSR YRTAVSARLG MLGVALLAYI LIIVAFLLGY DSTAGGWVP NDGAINIFST RYIEWTVSVP LLTIELLAVC ATLGVQARRN TAIAVTATGA MIFCGFLGAI VIDNGTNTGA F ILWAVISC ...String:
MRLTNVSVPW GATLSNAEHQ LIFYFLVVAA LAFVAGFIRT YITRNEVGSR YRTAVSARLG MLGVALLAYI LIIVAFLLGY DSTAGGWVP NDGAINIFST RYIEWTVSVP LLTIELLAVC ATLGVQARRN TAIAVTATGA MIFCGFLGAI VIDNGTNTGA F ILWAVISC VFWVIANVVL IRAVRQSLPT LTPESHTMLK SAAIVLLAGW VVYPIVYFLP LFGASGGLTT TILITLTVAD VI VKLGFST QTHRVAKLRT AEDVRAGDDV HPESIWISSV KQSDAGLPRE VYLAEGAAVH DRRTKPPTSA AVASPEAPLP PDS TPLDGG Y

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Macromolecule #2: EICOSANE

MacromoleculeName: EICOSANE / type: ligand / ID: 2 / Number of copies: 35 / Formula: LFA
Molecular weightTheoretical: 282.547 Da
Chemical component information

ChemComp-LFA:
EICOSANE

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Macromolecule #3: RETINAL

MacromoleculeName: RETINAL / type: ligand / ID: 3 / Number of copies: 5 / Formula: RET
Source (natural)Organism: Subtercola endophyticus (bacteria)
Molecular weightTheoretical: 284.436 Da
Chemical component information

ChemComp-RET:
RETINAL

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 155 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration7 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.1.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.44 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.2) / Number images used: 486732
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.1.2)

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