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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 / 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 / photoreceptor activity / phototransduction / photoreceptor outer segment ...Defective visual phototransduction due to OPN1MW loss of function / 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 / photoreceptor activity / phototransduction / photoreceptor outer segment / visual perception / electron transport chain / 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, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Science / Year: 2026
Title: Illuminating the molecular basis of human daylight vision
Authors: Schmidt, S.L. / Sen, S. / Isaikina, P.
History
DepositionJan 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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