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- PDB-9i3t: Dark-state structure of human medium-wave-sensitive cone opsin (O... -

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Basic information

Entry
Database: PDB / ID: 9i3t
TitleDark-state structure of human medium-wave-sensitive cone opsin (OPN1MW)
Components
  • BAG2 Anti-BRIL Fab Heavy Chain
  • BAG2 Anti-BRIL Fab Light Chain
  • Medium-wave-sensitive opsin 1,Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN / Human Cone opsin / GPCR / Retinal binding protein / Vision / Color perception
Function / homology
Function and homology information


Defective visual phototransduction due to OPN1MW 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 light stimulus / positive regulation of cytokinesis / phototransduction / photoreceptor activity ...Defective visual phototransduction due to OPN1MW 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 light stimulus / positive regulation of cytokinesis / phototransduction / photoreceptor activity / photoreceptor outer segment / visual perception / electron transport chain / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / photoreceptor disc membrane / G alpha (i) signalling events / electron transfer activity / periplasmic space / iron ion binding / G protein-coupled receptor signaling pathway / heme binding / identical protein binding / plasma membrane
Similarity search - Function
Opsin red/green sensitive / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / : / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. ...Opsin red/green sensitive / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / : / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / 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
RETINAL / Medium-wave-sensitive opsin 1 / Soluble cytochrome b562
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsSchmidt, S.L. / Sen, S. / Isaikina, P.
Funding supportEuropean Union, Switzerland, 2items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Swiss National Science Foundation Switzerland
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
DepositionJan 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
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Revision 1.1Jul 8, 2026Group: Author supporting evidence / Data collection / Database references
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Revision 1.1Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Medium-wave-sensitive opsin 1,Soluble cytochrome b562
H: BAG2 Anti-BRIL Fab Heavy Chain
L: BAG2 Anti-BRIL Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,9884
Polymers102,7033
Non-polymers2841
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Medium-wave-sensitive opsin 1,Soluble cytochrome b562 / Green cone photoreceptor pigment / Green-sensitive opsin / GOP / Cytochrome b-562


Mass: 54622.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Human medium-wavelength-sensitive opsin fused to soluble cytochrome b562 complex on the intracellular loop 3 (P0ABE7) and C-terminal 1D4 tag,Human medium-wavelength-sensitive opsin fused to ...Details: Human medium-wavelength-sensitive opsin fused to soluble cytochrome b562 complex on the intracellular loop 3 (P0ABE7) and C-terminal 1D4 tag,Human medium-wavelength-sensitive opsin fused to soluble cytochrome b562 complex on the intracellular loop 3 (P0ABE7) and C-terminal 1D4 tag,Human medium-wavelength-sensitive opsin fused to soluble cytochrome b562 complex on the intracellular loop 3 (P0ABE7) and C-terminal 1D4 tag
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: OPN1MW, GCP, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P04001, UniProt: P0ABE7
#2: Antibody BAG2 Anti-BRIL Fab Heavy Chain


Mass: 24539.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Antibody BAG2 Anti-BRIL Fab Light Chain


Mass: 23541.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human medium-wavelength-sensitive opsin fused to soluble cytochrome b562 in complex with BAG2 Fab
Type: COMPLEX / Entity ID: #2-#3 / Source: RECOMBINANT
Molecular weightValue: 0.102 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 6.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 137000 / Symmetry type: POINT
RefinementHighest resolution: 3.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0045058
ELECTRON MICROSCOPYf_angle_d0.6156894
ELECTRON MICROSCOPYf_dihedral_angle_d6.468700
ELECTRON MICROSCOPYf_chiral_restr0.041762
ELECTRON MICROSCOPYf_plane_restr0.005860

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