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- EMDB-53268: Pre-active dark-state structure of human short-wave-sensitive ops... -

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ID or keywords:

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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


cone photoreceptor disc membrane / Defective visual phototransduction due to OPN1SW loss of function / 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 ...cone photoreceptor disc membrane / Defective visual phototransduction due to OPN1SW loss of function / 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 / photoreceptor inner segment / visual perception / 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: Schmidt SL / Sen S / Isaikina P
History
DepositionMar 26, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53268.png

Downloads & links

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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 °

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Supplemental data

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Half map: #1

Fileemd_53268_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_53268_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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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

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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)

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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

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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

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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

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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

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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: 3.06 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)

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