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- EMDB-18796: Cryo-EM structure of the microbial rhodopsin CryoR1 at pH 8.0 in ... -

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Basic information

Entry
Database: EMDB / ID: EMD-18796
TitleCryo-EM structure of the microbial rhodopsin CryoR1 at pH 8.0 in nanodisc
Map data
Sample
  • Complex: Pentameric form of the microbial rhodopsin CryoR1
    • Protein or peptide: Rhodopsin
  • Ligand: EICOSANE
  • 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: 2.43 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: To Be Published
Title: CryoRhodopsins: a new clade of microbial rhodopsins from cold environments
Authors: Lamm GHU / Marin E / Schellbach AV / Stetsenko A / Alekseev A / Bourenkov G / Agthe M / Engilberge S / Rose S / Caramello N / Royant A / Schneider TR / Bateman A / Wachtveitl J / Guskov A / Kovalev K
History
DepositionOct 31, 2023-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18796.png

Downloads & links

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Map

FileDownload / File: emd_18796.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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.836 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.27
Minimum - Maximum-1.6415968 - 2.475538
Average (Standard dev.)-0.00069430197 (±0.045713697)
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: #1

Fileemd_18796_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_18796_half_map_2.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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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: EICOSANE
  • 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: in nanodisc, pH 8.0, ground 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: EICOSANE

MacromoleculeName: EICOSANE / type: ligand / ID: 2 / Number of copies: 20 / 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: 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: 240 / 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

Concentration2.7 mg/mL
BufferpH: 8
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: 0.8 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: 2.43 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.2) / Number images used: 218132
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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