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Yorodumi- EMDB-19884: Cryo-EM Structure of Jumping Spider Rhodopsin-1 bound to a Gi het... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19884 | |||||||||||||||
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Title | Cryo-EM Structure of Jumping Spider Rhodopsin-1 bound to a Gi heterotrimer | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | Opsin / GPCR / G protein / Signaling Complex / MEMBRANE PROTEIN | |||||||||||||||
Function / homology | Function and homology information Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / 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 ...Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / 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 / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / photoreceptor activity / phototransduction / T cell migration / D2 dopamine receptor binding / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / G protein-coupled serotonin receptor binding / cellular response to forskolin / regulation of mitotic spindle organization / visual perception / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Regulation of insulin secretion / G protein-coupled receptor binding / G protein-coupled receptor activity / 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 / G alpha (z) signalling events / ADORA2B mediated anti-inflammatory cytokines production / cellular response to catecholamine stimulus / adenylate cyclase-activating dopamine receptor signaling pathway / GPER1 signaling / GDP binding / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / signaling receptor complex adaptor activity / cell cortex / midbody / G alpha (i) signalling events / G alpha (s) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Extra-nuclear estrogen signaling / G protein-coupled receptor signaling pathway / lysosomal membrane / cell division / GTPase activity / centrosome / GTP binding / nucleolus / magnesium ion binding / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Hasarius adansoni (spider) / Homo sapiens (human) / Bos taurus (cattle) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.9 Å | |||||||||||||||
Authors | Tejero O / Pamula F / Koyanagi M / Nagata T / Afanasyev P / Das I / Deupi X / Sheves M / Terakita A / Schertler GFX ...Tejero O / Pamula F / Koyanagi M / Nagata T / Afanasyev P / Das I / Deupi X / Sheves M / Terakita A / Schertler GFX / Rodrigues MJ / Tsai C-J | |||||||||||||||
Funding support | European Union, Switzerland, 4 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Active state structures of a bistable visual opsin bound to G proteins. Authors: Oliver Tejero / Filip Pamula / Mitsumasa Koyanagi / Takashi Nagata / Pavel Afanasyev / Ishita Das / Xavier Deupi / Mordechai Sheves / Akihisa Terakita / Gebhard F X Schertler / Matthew J ...Authors: Oliver Tejero / Filip Pamula / Mitsumasa Koyanagi / Takashi Nagata / Pavel Afanasyev / Ishita Das / Xavier Deupi / Mordechai Sheves / Akihisa Terakita / Gebhard F X Schertler / Matthew J Rodrigues / Ching-Ju Tsai / Abstract: Opsins are G protein-coupled receptors (GPCRs) that have evolved to detect light stimuli and initiate intracellular signaling cascades. Their role as signal transducers is critical to light ...Opsins are G protein-coupled receptors (GPCRs) that have evolved to detect light stimuli and initiate intracellular signaling cascades. Their role as signal transducers is critical to light perception across the animal kingdom. Opsins covalently bind to the chromophore 11-cis retinal, which isomerizes to the all-trans isomer upon photon absorption, causing conformational changes that result in receptor activation. Monostable opsins, responsible for vision in vertebrates, release the chromophore after activation and must bind another retinal molecule to remain functional. In contrast, bistable opsins, responsible for non-visual light perception in vertebrates and for vision in invertebrates, absorb a second photon in the active state to return the chromophore and protein to the inactive state. Structures of bistable opsins in the activated state have proven elusive, limiting our understanding of how they function as bidirectional photoswitches. Here we present active state structures of a bistable opsin, jumping spider rhodopsin isoform-1 (JSR1), in complex with its downstream signaling partners, the G and G heterotrimers. These structures elucidate key differences in the activation mechanisms between monostable and bistable opsins, offering essential insights for the rational engineering of bistable opsins into diverse optogenetic tools to control G protein signaling pathways. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19884.map.gz | 144.4 MB | EMDB map data format | |
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Header (meta data) | emd-19884-v30.xml emd-19884.xml | 22.2 KB 22.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19884_fsc.xml | 14.3 KB | Display | FSC data file |
Images | emd_19884.png | 46.2 KB | ||
Filedesc metadata | emd-19884.cif.gz | 6.8 KB | ||
Others | emd_19884_half_map_1.map.gz emd_19884_half_map_2.map.gz | 194.2 MB 194.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19884 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19884 | HTTPS FTP |
-Validation report
Summary document | emd_19884_validation.pdf.gz | 813.4 KB | Display | EMDB validaton report |
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Full document | emd_19884_full_validation.pdf.gz | 812.9 KB | Display | |
Data in XML | emd_19884_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | emd_19884_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19884 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19884 | HTTPS FTP |
-Related structure data
Related structure data | 9eprMC 9eppC 9epqC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_19884.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8492 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_19884_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_19884_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Ternary complex of Jumping Spider Rhodopsin-1 with a human Gi het...
+Supramolecule #1: Ternary complex of Jumping Spider Rhodopsin-1 with a human Gi het...
+Supramolecule #2: Jumping Spider Rhodopsin-1
+Supramolecule #3: Guanine nucleotide-binding protein G(i) subunit alpha-1
+Supramolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
+Supramolecule #5: Guanine nucleotide-binding protein G(T) subunit gamma-T1
+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: Kumopsin1
+Macromolecule #5: RETINAL
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.00 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |