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Open data
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Basic information
Entry | Database: PDB / ID: 6oy9 | |||||||||
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Title | Structure of the Rhodopsin-Transducin Complex | |||||||||
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![]() | SIGNALING PROTEIN / GPCR / G protein / Complex | |||||||||
Function / homology | ![]() negative regulation of cyclic-nucleotide phosphodiesterase activity / Opsins / VxPx cargo-targeting to cilium / sperm head plasma membrane / rod bipolar cell differentiation / absorption of visible light / opsin binding / The canonical retinoid cycle in rods (twilight vision) / Olfactory Signaling Pathway / G protein-coupled opsin signaling pathway ...negative regulation of cyclic-nucleotide phosphodiesterase activity / Opsins / VxPx cargo-targeting to cilium / sperm head plasma membrane / rod bipolar cell differentiation / absorption of visible light / opsin binding / The canonical retinoid cycle in rods (twilight vision) / Olfactory Signaling Pathway / G protein-coupled opsin signaling pathway / photoreceptor inner segment membrane / Sensory perception of sweet, bitter, and umami (glutamate) taste / podosome assembly / G protein-coupled photoreceptor activity / 11-cis retinal binding / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / rod photoreceptor outer segment / cellular response to light stimulus / eye photoreceptor cell development / detection of light stimulus involved in visual perception / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / thermotaxis / Activation of the phototransduction cascade / outer membrane / detection of temperature stimulus involved in thermoception / response to light intensity / photoreceptor cell maintenance / arrestin family protein binding / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G alpha (12/13) signalling events / Glucagon-type ligand receptors / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Ca2+ pathway / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (s) signalling events / photoreceptor outer segment membrane / G alpha (q) signalling events / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / acyl binding / response to light stimulus / phototransduction, visible light / G-protein alpha-subunit binding / phototransduction / photoreceptor outer segment / sperm midpiece / photoreceptor inner segment / visual perception / guanyl-nucleotide exchange factor activity / G protein-coupled receptor binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / microtubule cytoskeleton organization / photoreceptor disc membrane / GDP binding / cellular response to catecholamine stimulus / adenylate cyclase-activating dopamine receptor signaling pathway / intracellular protein localization / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / cell-cell junction / sensory perception of taste / signaling receptor complex adaptor activity / retina development in camera-type eye / GTPase binding / phospholipase C-activating G protein-coupled receptor signaling pathway / gene expression / cell population proliferation / G protein-coupled receptor signaling pathway / Golgi membrane / GTPase activity / synapse / protein-containing complex binding / protein kinase binding / GTP binding / zinc ion binding / metal ion binding / identical protein binding / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
![]() | Gao, Y. / Hu, H. / Ramachandran, S. / Erickson, J.W. / Cerione, R.A. / Skiniotis, G. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of the Rhodopsin-Transducin Complex: Insights into G-Protein Activation. Authors: Yang Gao / Hongli Hu / Sekar Ramachandran / Jon W Erickson / Richard A Cerione / Georgios Skiniotis / ![]() Abstract: Rhodopsin (Rho), a prototypical G-protein-coupled receptor (GPCR) in vertebrate vision, activates the G-protein transducin (G) by catalyzing GDP-GTP exchange on its α subunit (Gα). To elucidate the ...Rhodopsin (Rho), a prototypical G-protein-coupled receptor (GPCR) in vertebrate vision, activates the G-protein transducin (G) by catalyzing GDP-GTP exchange on its α subunit (Gα). To elucidate the determinants of G coupling and activation, we obtained cryo-EM structures of a fully functional, light-activated Rho-G complex in the presence and absence of a G-protein-stabilizing nanobody. The structures illustrate how G overcomes its low basal activity by engaging activated Rho in a conformation distinct from other GPCR-G-protein complexes. Moreover, the nanobody-free structures reveal native conformations of G-protein components and capture three distinct conformers showing the Gα helical domain (αHD) contacting the Gβγ subunits. These findings uncover the molecular underpinnings of G-protein activation by visual rhodopsin and shed new light on the role played by Gβγ during receptor-catalyzed nucleotide exchange. | |||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 183.3 KB | Display | ![]() |
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PDB format | ![]() | 140.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 996.6 KB | Display | ![]() |
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Full document | ![]() | 1004.7 KB | Display | |
Data in XML | ![]() | 31.8 KB | Display | |
Data in CIF | ![]() | 47.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 20222MC ![]() 6oyaC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 41188.895 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 37430.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Protein | Mass: 9337.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#4: Protein | Mass: 39031.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#5: Chemical | ChemComp-RET / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Molecular weight | Value: 0.1418 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Image recording | Average exposure time: 8 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 12616 |
Image scans | Movie frames/image: 40 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 5872324 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 250451 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: BACKBONE TRACE |