+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4598 | ||||||||||||||||||
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Title | Rhodopsin-Gi protein complex | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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Function / homology | Function and homology information Opsins / VxPx cargo-targeting to cilium / opsin binding / rod bipolar cell differentiation / sperm head plasma membrane / Olfactory Signaling Pathway / absorption of visible light / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / The canonical retinoid cycle in rods (twilight vision) ...Opsins / VxPx cargo-targeting to cilium / opsin binding / rod bipolar cell differentiation / sperm head plasma membrane / Olfactory Signaling Pathway / absorption of visible light / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / The canonical retinoid cycle in rods (twilight vision) / 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 / response to light intensity / Activation of the phototransduction cascade / phototransduction, visible light / outer membrane / detection of temperature stimulus involved in thermoception / 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 / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thrombin signalling through proteinase activated receptors (PARs) / Ca2+ pathway / G alpha (z) signalling events / Extra-nuclear estrogen signaling / 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 / photoreceptor outer segment / G-protein alpha-subunit binding / response to light stimulus / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / regulation of mitotic spindle organization / cellular response to forskolin / sperm midpiece / visual perception / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / guanyl-nucleotide exchange factor activity / Regulation of insulin secretion / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / response to peptide hormone / ADP signalling through P2Y purinoceptor 12 / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / microtubule cytoskeleton organization / G alpha (z) signalling events / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / GPER1 signaling / GDP binding / G-protein beta-subunit binding / heterotrimeric G-protein complex / cell-cell junction / signaling receptor complex adaptor activity / gene expression / cell cortex / midbody / G alpha (i) signalling events / G alpha (s) signalling events / Extra-nuclear estrogen signaling / G protein-coupled receptor signaling pathway / cell division / Golgi membrane / lysosomal membrane / GTPase activity / centrosome Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) / Bos taurus (cattle) / Mus musculus (house mouse) / Bovine (cattle) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.38 Å | ||||||||||||||||||
Authors | Tsai C-J / Marino J / Adaixo RJ / Pamula F / Muehle J / Maeda S / Flock T / Taylor NMI / Mohammed I / Matile H ...Tsai C-J / Marino J / Adaixo RJ / Pamula F / Muehle J / Maeda S / Flock T / Taylor NMI / Mohammed I / Matile H / Dawson RJP / Deupi X / Stahlberg H / Schertler GFX | ||||||||||||||||||
Funding support | Switzerland, 5 items
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Citation | Journal: Elife / Year: 2019 Title: Cryo-EM structure of the rhodopsin-Gαi-βγ complex reveals binding of the rhodopsin C-terminal tail to the gβ subunit. Authors: Ching-Ju Tsai / Jacopo Marino / Ricardo Adaixo / Filip Pamula / Jonas Muehle / Shoji Maeda / Tilman Flock / Nicholas Mi Taylor / Inayatulla Mohammed / Hugues Matile / Roger Jp Dawson / ...Authors: Ching-Ju Tsai / Jacopo Marino / Ricardo Adaixo / Filip Pamula / Jonas Muehle / Shoji Maeda / Tilman Flock / Nicholas Mi Taylor / Inayatulla Mohammed / Hugues Matile / Roger Jp Dawson / Xavier Deupi / Henning Stahlberg / Gebhard Schertler / Abstract: One of the largest membrane protein families in eukaryotes are G protein-coupled receptors (GPCRs). GPCRs modulate cell physiology by activating diverse intracellular transducers, prominently ...One of the largest membrane protein families in eukaryotes are G protein-coupled receptors (GPCRs). GPCRs modulate cell physiology by activating diverse intracellular transducers, prominently heterotrimeric G proteins. The recent surge in structural data has expanded our understanding of GPCR-mediated signal transduction. However, many aspects, including the existence of transient interactions, remain elusive. We present the cryo-EM structure of the light-sensitive GPCR rhodopsin in complex with heterotrimeric Gi. Our density map reveals the receptor C-terminal tail bound to the Gβ subunit of the G protein, providing a structural foundation for the role of the C-terminal tail in GPCR signaling, and of Gβ as scaffold for recruiting Gα subunits and G protein-receptor kinases. By comparing available complexes, we found a small set of common anchoring points that are G protein-subtype specific. Taken together, our structure and analysis provide new structural basis for the molecular events of the GPCR signaling pathway. | ||||||||||||||||||
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_4598.map.gz | 9.7 MB | EMDB map data format | |
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Header (meta data) | emd-4598-v30.xml emd-4598.xml | 26.1 KB 26.1 KB | Display Display | EMDB header |
Images | emd_4598.png | 129.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4598 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4598 | HTTPS FTP |
-Validation report
Summary document | emd_4598_validation.pdf.gz | 207.1 KB | Display | EMDB validaton report |
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Full document | emd_4598_full_validation.pdf.gz | 206.2 KB | Display | |
Data in XML | emd_4598_validation.xml.gz | 6.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4598 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4598 | HTTPS FTP |
-Related structure data
Related structure data | 6qnoMC 6qnkC M: atomic model generated by this map C: citing same article (ref.) |
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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_4598.map.gz / Format: CCP4 / Size: 147.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.83 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-Gi complex bound with antibody fragment Fab16
+Supramolecule #1: Rhodopsin-Gi complex bound with antibody fragment Fab16
+Supramolecule #2: Guanine nucleotide-binding protein alpha subunit
+Supramolecule #3: Guanine nucleotide-binding protein beta/gamma subunit
+Supramolecule #4: antibody FAB fragment Fab16
+Supramolecule #5: Rhodopsin
+Macromolecule #1: Guanine nucleotide-binding protein G(i) subunit alpha-1
+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: Fab antibody fragment light chain
+Macromolecule #5: Fab antibody fragment heavy chain
+Macromolecule #6: Rhodopsin
+Macromolecule #8: RETINAL
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
Details: The detergent lauryl-maltose neopentyl glycol (LMNG) was used before the last purification step by gel filtration. In the gel filtration, detergent-free buffer was used. | |||||||||
Grid | Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV | |||||||||
Details | The sample was monodisperse. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 70.0 K / Max: 93.0 K |
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: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7676 pixel / Digitization - Dimensions - Height: 7420 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 3200 / Average exposure time: 10.0 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 25.0 µm / Calibrated defocus min: 15.0 µm / Calibrated magnification: 165000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 25.0 µm / Nominal defocus min: 15.0 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |