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Yorodumi- EMDB-37724: Human calcium-sensing receptor(CaSR) bound to cinacalcet in compl... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37724 | ||||||||||||
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Title | Human calcium-sensing receptor(CaSR) bound to cinacalcet in complex with Gq protein | ||||||||||||
Map data | composite reconstruction map of CaSR-Gq complex | ||||||||||||
Sample |
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Keywords | GPCR-G protein complex / allosteric modulator / activation / dimeric / MEMBRANE PROTEIN | ||||||||||||
Function / homology | Function and homology information bile acid secretion / chemosensory behavior / cellular response to peptide / response to fibroblast growth factor / cellular response to vitamin D / phosphatidylinositol phospholipase C activity / Class C/3 (Metabotropic glutamate/pheromone receptors) / calcium ion import / positive regulation of positive chemotaxis / fat pad development ...bile acid secretion / chemosensory behavior / cellular response to peptide / response to fibroblast growth factor / cellular response to vitamin D / phosphatidylinositol phospholipase C activity / Class C/3 (Metabotropic glutamate/pheromone receptors) / calcium ion import / positive regulation of positive chemotaxis / fat pad development / amino acid binding / cellular response to hepatocyte growth factor stimulus / branching morphogenesis of an epithelial tube / positive regulation of calcium ion import / regulation of calcium ion transport / cellular response to low-density lipoprotein particle stimulus / detection of calcium ion / anatomical structure morphogenesis / axon terminus / JNK cascade / positive regulation of vasoconstriction / chloride transmembrane transport / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / ossification / response to ischemia / G protein-coupled receptor activity / cellular response to glucose stimulus / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / positive regulation of insulin secretion / G-protein activation / G protein-coupled acetylcholine receptor signaling pathway / 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 / G beta:gamma signalling through CDC42 / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / intracellular calcium ion homeostasis / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / adenylate cyclase-activating dopamine receptor signaling pathway / vasodilation / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / G-protein beta-subunit binding / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / integrin binding / Thrombin signalling through proteinase activated receptors (PARs) / GTPase binding / retina development in camera-type eye / phospholipase C-activating G protein-coupled receptor signaling pathway / Ca2+ pathway / G alpha (i) signalling events / fibroblast proliferation / cellular response to hypoxia / G alpha (s) signalling events / G alpha (q) signalling events / basolateral plasma membrane / transmembrane transporter binding / cell population proliferation / Ras protein signal transduction / Extra-nuclear estrogen signaling / positive regulation of ERK1 and ERK2 cascade / G protein-coupled receptor signaling pathway / apical plasma membrane / lysosomal membrane / GTPase activity / neuronal cell body / synapse / calcium ion binding / positive regulation of cell population proliferation / positive regulation of gene expression / protein-containing complex binding / protein kinase binding / cell surface / signal transduction / protein homodimerization activity / extracellular exosome / identical protein binding Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / Rattus norvegicus (Norway rat) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
Authors | Ling SL / Meng XY / Tian CL | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: Cell Res / Year: 2024 Title: Structural insights into asymmetric activation of the calcium-sensing receptor-G complex. Authors: Shenglong Ling / Xianyu Meng / Yuan Zhang / Zhemin Xia / Yingxin Zhou / Fan Yang / Pan Shi / Chaowei Shi / Changlin Tian / | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37724.map.gz | 176.6 MB | EMDB map data format | |
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Header (meta data) | emd-37724-v30.xml emd-37724.xml | 24.1 KB 24.1 KB | Display Display | EMDB header |
Images | emd_37724.png | 116.1 KB | ||
Filedesc metadata | emd-37724.cif.gz | 7.4 KB | ||
Others | emd_37724_additional_1.map.gz emd_37724_additional_2.map.gz emd_37724_additional_3.map.gz | 168 MB 168 MB 167.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37724 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37724 | HTTPS FTP |
-Validation report
Summary document | emd_37724_validation.pdf.gz | 441.8 KB | Display | EMDB validaton report |
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Full document | emd_37724_full_validation.pdf.gz | 441.4 KB | Display | |
Data in XML | emd_37724_validation.xml.gz | 4.1 KB | Display | |
Data in CIF | emd_37724_validation.cif.gz | 4.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37724 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37724 | HTTPS FTP |
-Related structure data
Related structure data | 8wpuMC 8wpgC C: citing same article (ref.) M: atomic model generated by this map |
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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_37724.map.gz / Format: CCP4 / Size: 277.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | composite reconstruction map of CaSR-Gq complex | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: local refinement of G protein
File | emd_37724_additional_1.map | ||||||||||||
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Annotation | local refinement of G protein | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: reconstruction map of casr-Gq
File | emd_37724_additional_2.map | ||||||||||||
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Annotation | reconstruction map of casr-Gq | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: local refinement of CaSR receptor
File | emd_37724_additional_3.map | ||||||||||||
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Annotation | local refinement of CaSR receptor | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : CaSR-Gq complex
+Supramolecule #1: CaSR-Gq complex
+Macromolecule #1: Extracellular calcium-sensing receptor,calcium-sensing receptor
+Macromolecule #2: G subunit q (Gi2-mini-Gq chimeric)
+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: ScFv16
+Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #8: N-[(1R)-1-(naphthalen-1-yl)ethyl]-3-[3-(trifluoromethyl)phenyl]pr...
+Macromolecule #9: TRYPTOPHAN
+Macromolecule #10: CALCIUM ION
+Macromolecule #11: PHOSPHATE ION
+Macromolecule #12: CHOLESTEROL
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 7.0 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 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: 1.7 µm / Nominal defocus min: 1.3 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 239610 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |