[English] 日本語
Yorodumi
- EMDB-52707: Dark-state structure of human medium-wavelength cone opsin (OPN1MW) -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Supplemental images

emd_52707.png

Downloads & links

-
Map

FileReleased
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.574 Å
Density

Histogram

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 °

-
Supplemental data

-
Half map: #2

Fileemd_52707_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_52707_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 6.8
VitrificationCryogen name: ETHANE-PROPANE

-
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

+
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more