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- PDB-9yda: Cryo-EM structure of active human green cone opsin in complex wit... -

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Basic information

Entry
Database: PDB / ID: 9yda
TitleCryo-EM structure of active human green cone opsin in complex with chimeric G protein (miniGist)
Components
  • (Guanine nucleotide-binding protein ...) x 2
  • Genome polyprotein,Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas
  • Medium-wave-sensitive opsin 1
  • scFv16
KeywordsSIGNALING PROTEIN / G protein-coupled receptor / cone opsin
Function / homology
Function and homology information


Defective visual phototransduction due to OPN1MW loss of function / The retinoid cycle in cones (daylight vision) / Opsins / G protein-coupled photoreceptor activity / cellular response to light stimulus / positive regulation of cytokinesis / photoreceptor activity / phototransduction / photoreceptor outer segment / visual perception ...Defective visual phototransduction due to OPN1MW loss of function / The retinoid cycle in cones (daylight vision) / Opsins / G protein-coupled photoreceptor activity / cellular response to light stimulus / positive regulation of cytokinesis / photoreceptor activity / phototransduction / photoreceptor outer segment / visual perception / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through CDC42 / Glucagon signaling in metabolic regulation / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / ADP signalling through P2Y purinoceptor 12 / photoreceptor disc membrane / Sensory perception of sweet, bitter, and umami (glutamate) taste / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (z) signalling events / cellular response to catecholamine stimulus / ADP signalling through P2Y purinoceptor 1 / ADORA2B mediated anti-inflammatory cytokines production / G beta:gamma signalling through PI3Kgamma / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / adenylate cyclase-activating dopamine receptor signaling pathway / GPER1 signaling / G-protein beta-subunit binding / cellular response to prostaglandin E stimulus / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / G alpha (12/13) signalling events / sensory perception of taste / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / retina development in camera-type eye / GTPase binding / Ca2+ pathway / fibroblast proliferation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / G alpha (i) signalling events / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / Ras protein signal transduction / Extra-nuclear estrogen signaling / cell population proliferation / G protein-coupled receptor signaling pathway / lysosomal membrane / GTPase activity / synapse / protein-containing complex binding / signal transduction / extracellular exosome / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Opsin red/green sensitive / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / : / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily ...Opsin red/green sensitive / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / : / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
RETINAL / Medium-wave-sensitive opsin 1 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsYao, W. / Fay, J.F. / Farrens, D.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)R01 EY029343A United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structure of human green cone opsin yields insights into mechanisms underlying the rapid decay of its active, signaling state.
Authors: Weekie Yao / Jonathan F Fay / David L Farrens /
Abstract: Cone opsins enable daylight vision and color discrimination. Like their dim-light cousin rhodopsin (Rho) found in rod cells, they use a covalently attached retinal ligand to sense light and initiate ...Cone opsins enable daylight vision and color discrimination. Like their dim-light cousin rhodopsin (Rho) found in rod cells, they use a covalently attached retinal ligand to sense light and initiate visual phototransduction by activating G proteins. Unfortunately, we know less about their structural properties, in part because their activated state is unstable-cone opsins release their retinal agonist within seconds after light activation, ~100× faster than Rho. To determine what causes this rapid release and how it affects G protein activation, we solved the structure of active-state, wild-type human green cone opsin (GCO) stabilized with a mini-G protein and then compared its structural and biophysical properties to Rho. Our results reveal unique features in the active-state GCO structure. These include i) a larger water channel connected to a larger retinal binding cavity, ii) a larger "hole" near the retinal Schiff base that could facilitate both retinal escape and water access; and iii) a potential anionic residue, E102, that lies within ~3.6 Å of the Schiff base. Our biophysical assays show that neutralizing E102 (mutant GCO) slows retinal release (~8×) from the receptor and increases G protein activation. Surprisingly, our kinetic studies suggest that entropic factors are the main cause for the faster retinal release from activated GCO. These unique attributes in GCO likely facilitate its function in bright daylight. These results support the proposal that rapid retinal release from an active-state cone opsin helps prevent signal saturation and enables rapid resetting of the receptor.
History
DepositionSep 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data 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
R: Medium-wave-sensitive opsin 1
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
G: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
H: scFv16
A: Genome polyprotein,Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,8906
Polymers172,6055
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

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Protein , 2 types, 2 molecules RA

#1: Protein Medium-wave-sensitive opsin 1 / Green cone photoreceptor pigment / Green-sensitive opsin / GOP


Mass: 40700.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: wild-type human green cone opsin with Rho1D4 tail / Source: (gene. exp.) Homo sapiens (human) / Gene: OPN1MW, GCP / Plasmid: pMT4 / Cell (production host): fibroblast / Cell line (production host): COS-1 / Production host: Chlorocebus aethiops (grivet) / Tissue (production host): kidney / References: UniProt: P04001
#5: Protein Genome polyprotein,Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas


Mass: 57380.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pcDNA3 / Cell (production host): fibroblast / Cell line (production host): COS-1 / Production host: Chlorocebus aethiops (grivet) / Tissue (production host): kidney
References: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement

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Guanine nucleotide-binding protein ... , 2 types, 2 molecules BG

#2: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 38878.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: G beta 1 subunit with Rho1D4 tail / Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Plasmid: pcDNA3 / Cell (production host): fibroblast / Cell line (production host): COS-1 / Production host: Chlorocebus aethiops (grivet) / Tissue (production host): kidney / References: UniProt: P62873
#3: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 7861.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNG2 / Plasmid: pcDNA3 / Cell (production host): fibroblast / Cell line (production host): COS-1 / Production host: Chlorocebus aethiops (grivet) / Tissue (production host): kidney / References: UniProt: P59768

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Antibody / Non-polymers , 2 types, 2 molecules H

#4: Antibody scFv16


Mass: 27784.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
#6: Chemical ChemComp-RET / RETINAL


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

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Details

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: Cryo-EM structure of active human green cone opsin in complex with chimeric G protein (miniGist)
Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Chlorocebus aethiops (grivet) / Cell: COS-1 / Plasmid: pcDNA3
Buffer solutionpH: 7
Buffer componentConc.: 20 mM / Name: HEPES / Formula: C8H18N2O4S
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2100 nm / Nominal defocus min: 200 nm
Image recordingElectron dose: 37.2 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 4190

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
7UCSF ChimeraXmodel fitting
9PHENIXmodel refinement
10Cootmodel refinement
11Rosettamodel refinement
15cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 639873 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model

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