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- EMDB-52707: Dark-state structure of human medium-wavelength cone opsin (OPN1MW) -

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Basic information

Entry
Database: EMDB / ID: EMD-52707
TitleDark-state structure of human medium-wavelength cone opsin (OPN1MW)
Map data
Sample
  • Complex: Human medium-wavelength-sensitive opsin fused to soluble cytochrome b562 in complex with BAG2 Fab
KeywordsHuman Cone opsin / GPCR / Retinal binding protein / Vision / Color perception / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsSchmidt SL / Isaikina P
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Science / Year: 2026
Title: Illuminating the molecular basis of human daylight vision.
Authors: Sarah L Schmidt / Jakub Dostal / Saumik Sen / Andrej Hovan / Deborah Walter / Martin V Appleby / Asato Kojima / Hideaki E Kato / John H Beale / Miroslav Kloz / Gebhard F X Schertler / Polina Isaikina /
Abstract: Photopic vision, including fast motion and color perception in daylight, is mediated by cone opsins, specialized G protein-coupled receptors (GPCRs). Despite sharing the same chromophore, the three ...Photopic vision, including fast motion and color perception in daylight, is mediated by cone opsins, specialized G protein-coupled receptors (GPCRs). Despite sharing the same chromophore, the three receptor subtypes absorb light at different wavelengths of the visible spectrum. The molecular mechanisms governing their spectral properties and exceptionally rapid responses remain largely unknown. We report cryo-electron microscopy structures of the human blue-sensitive (OPN1SW) and green-sensitive (OPN1MW) cone opsins in their dark-adapted states, combined with femtosecond-resolution spectroscopy, functional assays, and advanced simulations. The data reveal distinct chromophore stabilization mechanisms across human visual opsins and specific sequence adaptations in the GPCR microswitch motifs, underlining their structural plasticity and distinct activation mechanisms. These findings delineate the molecular basis of the evolutionary refinements fulfilling the needs of vision in daylight.
History
DepositionFeb 4, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52707.png

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Map

FileDownload / File: emd_52707.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 512 pix.
= 293.888 Å		0.57 Å/pix.
x 512 pix.
= 293.888 Å		0.57 Å/pix.
x 512 pix.
= 293.888 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.574 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.38170025 - 0.57613695
Average (Standard dev.)0.00007002781 (±0.005257516)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 293.888 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_52707_half_map_1.map
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Half map: #1

Fileemd_52707_half_map_2.map
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Sample components

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Entire : Human medium-wavelength-sensitive opsin fused to soluble cytochro...

EntireName: Human medium-wavelength-sensitive opsin fused to soluble cytochrome b562 in complex with BAG2 Fab
Components
  • Complex: Human medium-wavelength-sensitive opsin fused to soluble cytochrome b562 in complex with BAG2 Fab

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Supramolecule #1: Human medium-wavelength-sensitive opsin fused to soluble cytochro...

SupramoleculeName: Human medium-wavelength-sensitive opsin fused to soluble cytochrome b562 in complex with BAG2 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 102 KDa

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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

BufferpH: 6.8
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 137000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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