[English] 日本語
Yorodumi
- EMDB-53268: Pre-active dark-state structure of human short-wave-sensitive ops... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53268
TitlePre-active dark-state structure of human short-wave-sensitive opsin (OPN1SW)
Map data
Sample
  • Complex: Human short-wave-sensitive opsin fused to soluble cytochrome b562 in complex with SPR2070 Fab
    • Protein or peptide: Short-wave-sensitive opsin 1,Soluble cytochrome b562
    • Protein or peptide: Light chain BRIL Fab SRP2070
    • Protein or peptide: Heavy chain BRIL Fab SRP2070
  • Ligand: RETINAL
Keywordshuman daylight vision / GPCR / OPN1SW / blue cone opsin / MEMBRANE PROTEIN
Function / homology
Function and homology information


Defective visual phototransduction due to OPN1SW loss of function / cone photoreceptor disc membrane / The retinoid cycle in cones (daylight vision) / Opsins / absorption of visible light / G protein-coupled photoreceptor activity / cellular response to UV-A / cellular response to light stimulus / phototransduction / photoreceptor outer segment ...Defective visual phototransduction due to OPN1SW loss of function / cone photoreceptor disc membrane / The retinoid cycle in cones (daylight vision) / Opsins / absorption of visible light / G protein-coupled photoreceptor activity / cellular response to UV-A / cellular response to light stimulus / phototransduction / photoreceptor outer segment / visual perception / photoreceptor inner segment / electron transport chain / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / photoreceptor disc membrane / signaling receptor activity / G alpha (i) signalling events / electron transfer activity / periplasmic space / iron ion binding / G protein-coupled receptor signaling pathway / heme binding / perinuclear region of cytoplasm / signal transduction / plasma membrane
Similarity search - Function
Opsin, blue sensitive / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / : / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) ...Opsin, blue sensitive / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / : / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
Short-wave-sensitive opsin 1 / Soluble cytochrome b562
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 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
DepositionMar 26, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_53268.png

Downloads & links

-
Map

FileDownload / File: emd_53268.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 480 pix.
= 351.36 Å		0.73 Å/pix.
x 480 pix.
= 351.36 Å		0.73 Å/pix.
x 480 pix.
= 351.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.732 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.103
Minimum - Maximum-1.1164767 - 1.631261
Average (Standard dev.)-0.00008030884 (±0.012563778)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 351.36 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_53268_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_53268_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human short-wave-sensitive opsin fused to soluble cytochrome b562...

EntireName: Human short-wave-sensitive opsin fused to soluble cytochrome b562 in complex with SPR2070 Fab
Components
  • Complex: Human short-wave-sensitive opsin fused to soluble cytochrome b562 in complex with SPR2070 Fab
    • Protein or peptide: Short-wave-sensitive opsin 1,Soluble cytochrome b562
    • Protein or peptide: Light chain BRIL Fab SRP2070
    • Protein or peptide: Heavy chain BRIL Fab SRP2070
  • Ligand: RETINAL

-
Supramolecule #1: Human short-wave-sensitive opsin fused to soluble cytochrome b562...

SupramoleculeName: Human short-wave-sensitive opsin fused to soluble cytochrome b562 in complex with SPR2070 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Short-wave-sensitive opsin 1,Soluble cytochrome b562

MacromoleculeName: Short-wave-sensitive opsin 1,Soluble cytochrome b562 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.49475 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSEEEFYLFK NISSVGPWDG PQYHIAPVWA FYLQAAFMGT VFLIGFPLNA MVLVATLRYK KLRQPLNYIL VNVSFGGFLL CIFSVFPVF VASCNGYFVF GRHVCALEGF LGTVAGLVTG WSLAFLAFER YIVICKPFGN FRFSSKHALT VVLATWTIGI G VSIPPFFG ...String:
MSEEEFYLFK NISSVGPWDG PQYHIAPVWA FYLQAAFMGT VFLIGFPLNA MVLVATLRYK KLRQPLNYIL VNVSFGGFLL CIFSVFPVF VASCNGYFVF GRHVCALEGF LGTVAGLVTG WSLAFLAFER YIVICKPFGN FRFSSKHALT VVLATWTIGI G VSIPPFFG WSRFIPEGLQ CSCGPDWYTV GTKYRSESYT WFLFIFCFIV PLSLICFSYT QLLRALKAVA AQARRQLADL ED NWETLND NLKVIEKADN AAQVKDALTK MRAAALDAQK ATPPKLEDKS PDSPEMKDFR HGFDILVGQI DDALKLANEG KVK EAQAAA EQLKTTRNAY IQKYLRSTLQ ESATTQKAER EVSRMVVVMV GSFCVCYVPY AAFAMYMVNN RNHGLDLRLV TIPS FFSKS ACIYNPIIYC FMNKQFQACI MKMVCGKAMT DESDTCSSQK TEVSTVSSTQ VGPNLEVLFQ GPDYKDDDDK GAGAT ETSQ VAPA

UniProtKB: Short-wave-sensitive opsin 1, Soluble cytochrome b562, Short-wave-sensitive opsin 1

-
Macromolecule #2: Light chain BRIL Fab SRP2070

MacromoleculeName: Light chain BRIL Fab SRP2070 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 23.812252 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MDIVLTQSPA TLSVTPGDRV SLSCRASQSV SNYLHWYQQK SHESPRLLIK YASQSISGIP SRFSGSGSGT DFTLSINSVE TEDFGMYFC QQSNSWPLTF GAGTKLELRR ADAAPTVSIF PPSSEQLTSG GASVVCFLNN FYPKDINVKW KIDGSERQNG V LNSWTDQD ...String:
MDIVLTQSPA TLSVTPGDRV SLSCRASQSV SNYLHWYQQK SHESPRLLIK YASQSISGIP SRFSGSGSGT DFTLSINSVE TEDFGMYFC QQSNSWPLTF GAGTKLELRR ADAAPTVSIF PPSSEQLTSG GASVVCFLNN FYPKDINVKW KIDGSERQNG V LNSWTDQD SKDSTYSMSS TLTLTKDEYE RHNSYTCEAT HKTSTSPIVK SFNRNEC

-
Macromolecule #3: Heavy chain BRIL Fab SRP2070

MacromoleculeName: Heavy chain BRIL Fab SRP2070 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 24.033934 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MQIQLQQSGP ELVKPGASVK ISCKASGYTF TDFYINWMKQ RPGQGLEWIG WIFPGSGNTH YNEKFKGKAT LIVDTSSSTA FMQLNSLTS EDSAVYFCTR PVSYYYDFDY WGQGTTLTVS SAKTTAPSVY PLAPVCGDTS GSSVTLGCLV KGYFPEPVTL T WNSGSLSS ...String:
MQIQLQQSGP ELVKPGASVK ISCKASGYTF TDFYINWMKQ RPGQGLEWIG WIFPGSGNTH YNEKFKGKAT LIVDTSSSTA FMQLNSLTS EDSAVYFCTR PVSYYYDFDY WGQGTTLTVS SAKTTAPSVY PLAPVCGDTS GSSVTLGCLV KGYFPEPVTL T WNSGSLSS GVHTFPAVLQ SDLYTLSSSV TVTSSTWPSQ SITCNVAHPA SSTKVDKKIE PRGC

-
Macromolecule #4: RETINAL

MacromoleculeName: RETINAL / type: ligand / ID: 4 / Number of copies: 1 / Formula: RET
Molecular weightTheoretical: 284.436 Da
Chemical component information

ChemComp-RET:
RETINAL

-
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: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 520899
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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