+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20223 | ||||||||||||
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Title | Structure of the Rhodopsin-Transducin-Nanobody Complex | ||||||||||||
Map data | Rhodopsin-Transducin-Nanobody Complex | ||||||||||||
Sample |
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Function / homology | Function and homology information detection of light stimulus involved in visual perception / negative regulation of cyclic-nucleotide phosphodiesterase activity / Opsins / VxPx cargo-targeting to cilium / opsin binding / rod bipolar cell differentiation / sperm head plasma membrane / absorption of visible light / Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste ...detection of light stimulus involved in visual perception / negative regulation of cyclic-nucleotide phosphodiesterase activity / Opsins / VxPx cargo-targeting to cilium / opsin binding / rod bipolar cell differentiation / sperm head plasma membrane / absorption of visible light / Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / The canonical retinoid cycle in rods (twilight vision) / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / G protein-coupled opsin signaling pathway / photoreceptor inner segment membrane / podosome assembly / 11-cis retinal binding / G protein-coupled photoreceptor activity / rod photoreceptor outer segment / cellular response to light stimulus / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / thermotaxis / Activation of the phototransduction cascade / phototransduction, visible light / response to light intensity / outer membrane / detection of temperature stimulus involved in thermoception / arrestin family protein binding / photoreceptor cell maintenance / 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 / Glucagon-type ligand receptors / G alpha (12/13) signalling events / 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 / Thrombin signalling through proteinase activated receptors (PARs) / Ca2+ pathway / Extra-nuclear estrogen signaling / G alpha (z) signalling events / G alpha (s) signalling events / G alpha (q) signalling events / photoreceptor outer segment membrane / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / phototransduction / response to light stimulus / photoreceptor outer segment / acyl binding / G-protein alpha-subunit binding / sperm midpiece / visual perception / photoreceptor inner segment / G-protein beta/gamma-subunit complex binding / guanyl-nucleotide exchange factor activity / G protein-coupled receptor binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / microtubule cytoskeleton organization / photoreceptor disc membrane / cellular response to catecholamine stimulus / adenylate cyclase-activating dopamine receptor signaling pathway / GDP binding / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / cell-cell junction / signaling receptor complex adaptor activity / gene expression / G protein-coupled receptor signaling pathway / Golgi membrane / GTPase activity / GTP binding / protein kinase binding / zinc ion binding / identical protein binding / membrane / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Bos taurus (cattle) / Lama glama (llama) / Bovine (cattle) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||
Authors | Gao Y / Hu H / Ramachandran S / Erickson JW / Cerione RA / Skiniotis G | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Mol Cell / Year: 2019 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
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20223.map.gz | 48.9 MB | EMDB map data format | |
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Header (meta data) | emd-20223-v30.xml emd-20223.xml | 18.8 KB 18.8 KB | Display Display | EMDB header |
Images | emd_20223.png | 122.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20223 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20223 | HTTPS FTP |
-Validation report
Summary document | emd_20223_validation.pdf.gz | 488.2 KB | Display | EMDB validaton report |
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Full document | emd_20223_full_validation.pdf.gz | 487.8 KB | Display | |
Data in XML | emd_20223_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | emd_20223_validation.cif.gz | 7.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20223 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20223 | HTTPS FTP |
-Related structure data
Related structure data | 6oyaMC 6oy9C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_20223.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Rhodopsin-Transducin-Nanobody Complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Rhodopsin-Transducin-Nanobody Complex
+Supramolecule #1: Rhodopsin-Transducin-Nanobody Complex
+Supramolecule #2: Transducin
+Supramolecule #3: Rhodopsin
+Supramolecule #4: Nanobody
+Macromolecule #1: Gt-alpha/Gi1-alpha chimera
+Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
+Macromolecule #3: Guanine nucleotide-binding protein G(T) subunit gamma-T1
+Macromolecule #4: Camelid antibody VHH fragment
+Macromolecule #5: Rhodopsin
+Macromolecule #6: RETINAL
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III Details: Blot for 1 second before plunging; avoid light as much as possible.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 3837 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: Gctf (ver. 1.06) |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 309116 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Protocol: BACKBONE TRACE |
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Output model | PDB-6oya: |