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- EMDB-18799: Cryo-EM structure of the microbial rhodopsin CryoR1 at pH 10.5 in... -

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Basic information

Entry
Database: EMDB / ID: EMD-18799
TitleCryo-EM structure of the microbial rhodopsin CryoR1 at pH 10.5 in detergent in the M state
Map data
Sample
  • Complex: Pentameric form of the microbial rhodopsin CryoR1
    • Protein or peptide: Rhodopsin
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: RETINAL
  • Ligand: water
Keywordsrhodopsin / retinal / cryo-EM / light sensor / MEMBRANE PROTEIN
Function / homologyBacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / photoreceptor activity / phototransduction / membrane / Rhodopsin
Function and homology information
Biological speciesCryobacterium levicorallinum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 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_18799.png

Downloads & links

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Map

FileDownload / File: emd_18799.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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AxesZ (Sec.)Y (Row.)X (Col.)
0.42 Å/pix.
x 640 pix.
= 267.52 Å		0.42 Å/pix.
x 640 pix.
= 267.52 Å		0.42 Å/pix.
x 640 pix.
= 267.52 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.418 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.3860685 - 0.63963145
Average (Standard dev.)0.000028218552 (±0.016959958)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 267.52002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_18799_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_18799_half_map_2.map
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Sample components

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Entire : Pentameric form of the microbial rhodopsin CryoR1

EntireName: Pentameric form of the microbial rhodopsin CryoR1
Components
  • Complex: Pentameric form of the microbial rhodopsin CryoR1
    • Protein or peptide: Rhodopsin
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: RETINAL
  • Ligand: water

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Supramolecule #1: Pentameric form of the microbial rhodopsin CryoR1

SupramoleculeName: Pentameric form of the microbial rhodopsin CryoR1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Solubilized in DDM, pH 10.5, M state of CryoR1
Source (natural)Organism: Cryobacterium levicorallinum (bacteria)
Molecular weightTheoretical: 182 KDa

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Macromolecule #1: Rhodopsin

MacromoleculeName: Rhodopsin / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Cryobacterium levicorallinum (bacteria)
Molecular weightTheoretical: 35.206965 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTDMISAPWE ASLTQAEHSL IFYFLALTGS ALLFGLARTW LTRGEVGARY RTAVVARSGI MIVATLSYVF MVLAFTSGYD HVGSLWVPN SEAIMTIAPR YVEWSIAVPL LSIELLSVAT LSGVSARRTR LAAVAGAFLM IFTGFLGAVV IGDGRSVGSL I IWGAISTV ...String:
MTDMISAPWE ASLTQAEHSL IFYFLALTGS ALLFGLARTW LTRGEVGARY RTAVVARSGI MIVATLSYVF MVLAFTSGYD HVGSLWVPN SEAIMTIAPR YVEWSIAVPL LSIELLSVAT LSGVSARRTR LAAVAGAFLM IFTGFLGAVV IGDGRSVGSL I IWGAISTV FWIITAVILI RAIRHSLPQL TPEAAALLKT ATIFLMSGWA VYPLAYLIQI LFAGGLWTTS IHIILCTADI VV KLGFCGL IHRIAKLRTA EDVRAGVDIH TEAIWISSVK QSDAGIPTVV YLPEGETIHQ RRPKPSDSNA TASSSARQWT DDF PPTDL

UniProtKB: Rhodopsin

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Macromolecule #2: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 2 / Number of copies: 5 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #3: RETINAL

MacromoleculeName: RETINAL / type: ligand / ID: 3 / Number of copies: 5 / Formula: RET
Source (natural)Organism: Cryobacterium levicorallinum (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: 343 / 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: 10.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300
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: 1.2 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: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.2) / Number images used: 541978
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2)

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