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- EMDB-52615: Dark-state structure of human medium-wave-sensitive cone opsin (O... -

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Basic information

Entry
Database: EMDB / ID: EMD-52615
TitleDark-state structure of human medium-wave-sensitive cone opsin (OPN1MW)
Map dataDeepEM enhanced map Composite map
Sample
  • Complex: Human medium-wavelength-sensitive opsin fused to soluble cytochrome b562 in complex with BAG2 Fab
    • Protein or peptide: BAG2 Anti-BRIL Fab Heavy Chain
    • Protein or peptide: BAG2 Anti-BRIL Fab Light Chain
  • Protein or peptide: Medium-wave-sensitive opsin 1,Soluble cytochrome b562
  • Ligand: RETINAL
KeywordsHuman Cone opsin / GPCR / Retinal binding protein / Vision / Color perception / MEMBRANE PROTEIN
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
Medium-wave-sensitive opsin 1 / Soluble cytochrome b562
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 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
DepositionJan 24, 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_52615.png

Downloads & links

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Map

FileDownload / File: emd_52615.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEM enhanced map Composite map
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: 0.05
Minimum - Maximum-0.36847284 - 3.2752604
Average (Standard dev.)0.00055936544 (±0.01896105)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 293.888 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52615_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focused refinement map

Fileemd_52615_additional_1.map
AnnotationFocused refinement map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52615_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52615_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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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
    • Protein or peptide: BAG2 Anti-BRIL Fab Heavy Chain
    • Protein or peptide: BAG2 Anti-BRIL Fab Light Chain
  • Protein or peptide: Medium-wave-sensitive opsin 1,Soluble cytochrome b562
  • Ligand: RETINAL

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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: #2-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 102 KDa

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

MacromoleculeName: Medium-wave-sensitive opsin 1,Soluble cytochrome b562 / type: protein_or_peptide / ID: 1
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
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.622645 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAQQWSLQRL AGRHPQDSYE DSTQSSIFTY TNSNSTRGPF EGPNYHIAPR WVYHLTSVWM IFVVIASVFT NGLVLAATMK FKKLRHPLN WILVNLAVAD LAETVIASTI SVVNQVYGYF VLGHPMCVLE GYTVSLCGIT GLWSLAIISW ERWMVVCKPF G NVRFDAKL ...String:
MAQQWSLQRL AGRHPQDSYE DSTQSSIFTY TNSNSTRGPF EGPNYHIAPR WVYHLTSVWM IFVVIASVFT NGLVLAATMK FKKLRHPLN WILVNLAVAD LAETVIASTI SVVNQVYGYF VLGHPMCVLE GYTVSLCGIT GLWSLAIISW ERWMVVCKPF G NVRFDAKL AIVGIAFSWI WAAVWTAPPI FGWSRYWPHG LKTSCGPDVF SGSSYPGVQS YMIVLMVTCC ITPLSIIVLC YL QVWLAIA DLEDNWETLN DNLKVIEKAD NAAQVKDALT KMRAAALDAQ KATPPKLEDK SPDSPEMKDF RHGFDILVGQ IDD ALKLAN EGKVKEAQAA AEQLKTTRNA YIQKYLKESE STQKAEKEVT RMVVVMVLAF CFCWGPYAFF ACFAAANPGY PFHP LMAAL PAFFAKSATI YNPVIYVFMN RQFRNCILQL FGKKVDDGSE LSSASKTEVS SVSSVSPALE VLFQGPDYKD DDDKG AGAT ETSQVAPA

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

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Macromolecule #2: BAG2 Anti-BRIL Fab Heavy Chain

MacromoleculeName: BAG2 Anti-BRIL Fab Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 24.539314 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVVDFSLHWV RQAPGKGLEW VAYISSSSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARWGYWPGEP WWKAFDYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NVVDFSLHWV RQAPGKGLEW VAYISSSSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARWGYWPGEP WWKAFDYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SCD

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Macromolecule #3: BAG2 Anti-BRIL Fab Light Chain

MacromoleculeName: BAG2 Anti-BRIL Fab Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 23.541164 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQ QYLYYSLVTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQ QYLYYSLVTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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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
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
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: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 137000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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