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Yorodumi- EMDB-19883: Cryo-EM Structure of Jumping Spider Rhodopsin-1 bound to a Giq he... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19883 | |||||||||||||||
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Title | Cryo-EM Structure of Jumping Spider Rhodopsin-1 bound to a Giq heterotrimer | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | Opsin / GPCR / G protein / Signaling Complex / MEMBRANE PROTEIN | |||||||||||||||
Function / homology | Function and homology information photoreceptor activity / phototransduction / T cell migration / 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 ...photoreceptor activity / phototransduction / T cell migration / 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 / 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 / Olfactory Signaling Pathway / Activation of the phototransduction cascade / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / response to peptide hormone / G beta:gamma signalling through CDC42 / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / adenylate cyclase-activating dopamine receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / GDP binding / cellular response to prostaglandin E stimulus / Inactivation, recovery and regulation of the phototransduction cascade / G-protein beta-subunit binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / GTPase binding / retina development in camera-type eye / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / cell cortex / midbody / fibroblast proliferation / G alpha (i) signalling events / G alpha (s) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / G alpha (q) signalling events / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / G protein-coupled receptor signaling pathway / cell division / lysosomal membrane / GTPase activity / centrosome / synapse / protein-containing complex binding / nucleolus / GTP binding / magnesium ion binding / signal transduction / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Hasarius adansoni (spider) / Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.15 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_19883.map.gz | 49.7 MB | EMDB map data format | |
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Header (meta data) | emd-19883-v30.xml emd-19883.xml | 21.6 KB 21.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19883_fsc.xml | 8 KB | Display | FSC data file |
Images | emd_19883.png | 60.9 KB | ||
Filedesc metadata | emd-19883.cif.gz | 6.8 KB | ||
Others | emd_19883_half_map_1.map.gz emd_19883_half_map_2.map.gz | 48.9 MB 48.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19883 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19883 | HTTPS FTP |
-Validation report
Summary document | emd_19883_validation.pdf.gz | 782.8 KB | Display | EMDB validaton report |
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Full document | emd_19883_full_validation.pdf.gz | 782.3 KB | Display | |
Data in XML | emd_19883_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | emd_19883_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19883 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19883 | HTTPS FTP |
-Related structure data
Related structure data | 9epqMC 9eppC 9eprC 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_19883.map.gz / Format: CCP4 / Size: 52.7 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: 1.02 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_19883_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_19883_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 chimeric Giq...
+Supramolecule #1: Ternary complex of Jumping Spider Rhodopsin-1 with a chimeric Giq...
+Supramolecule #2: Jumping Spider Rhodopsin-1
+Supramolecule #3: Human Gi/Jumping Spider Gq Chimera
+Supramolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
+Supramolecule #5: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
+Macromolecule #1: Kumopsin1
+Macromolecule #2: Guanine nucleotide-binding protein G(i) subunit alpha-1
+Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
+Macromolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
+Macromolecule #5: 11,20-Ethanoretinal
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 8.5 mg/mL |
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Buffer | pH: 6.5 |
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: 70.0 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 / Nominal magnification: 165000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |