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Yorodumi- EMDB-34947: Structure of a GPCR-G protein in complex with a natural peptide a... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34947 | |||||||||
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Title | Structure of a GPCR-G protein in complex with a natural peptide agonist | |||||||||
Map data | Full map corresponding to C5a-C5aR1-Go | |||||||||
Sample |
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Keywords | GPCR / G protein / SIGNALING PROTEIN / SIGNALING PROTEIN-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information complement component C5a binding / cell proliferation in hindbrain / complement component C5a signaling pathway / presynapse organization / regulation of tau-protein kinase activity / Peptide ligand-binding receptors / complement component C5a receptor activity / Regulation of Complement cascade / response to peptidoglycan / Terminal pathway of complement ...complement component C5a binding / cell proliferation in hindbrain / complement component C5a signaling pathway / presynapse organization / regulation of tau-protein kinase activity / Peptide ligand-binding receptors / complement component C5a receptor activity / Regulation of Complement cascade / response to peptidoglycan / Terminal pathway of complement / membrane attack complex / G alpha (i) signalling events / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / complement receptor mediated signaling pathway / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / positive regulation of neutrophil chemotaxis / complement activation, alternative pathway / chemokine activity / dopamine receptor signaling pathway / endopeptidase inhibitor activity / positive regulation of macrophage chemotaxis / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production / G protein-coupled serotonin receptor binding / complement activation, classical pathway / positive regulation of chemokine production / Neutrophil degranulation / Peptide ligand-binding receptors / neutrophil chemotaxis / muscle contraction / positive regulation of epithelial cell proliferation / Regulation of Complement cascade / astrocyte activation / G protein-coupled receptor activity / microglial cell activation / Olfactory Signaling Pathway / G-protein beta/gamma-subunit complex binding / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / mRNA transcription by RNA polymerase II / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / 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 / cognition / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / sensory perception of taste / GPER1 signaling / G-protein beta-subunit binding / positive regulation of angiogenesis / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / chemotaxis / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / retina development in camera-type eye / apical part of cell / GTPase binding / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / fibroblast proliferation / G alpha (s) signalling events / cytoplasmic vesicle / G alpha (q) signalling events / basolateral plasma membrane / killing of cells of another organism / Ras protein signal transduction / cell population proliferation / negative regulation of neuron apoptotic process / Extra-nuclear estrogen signaling / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.89 Å | |||||||||
Authors | Saha S / Maharana J / Yadav MK / Sarma P / Chami M / Banerjee R / Shukla AK | |||||||||
Funding support | India, 1 items
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Citation | Journal: Cell(Cambridge,Mass.) / Year: 2023 Title: Structure of a GPCR-G protein in complex with a synthetic peptide agonist Authors: Saha S / Maharana J / Yadav MK / Sarma P / Chami M / Banerjee R / Shukla AK | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34947.map.gz | 168 MB | EMDB map data format | |
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Header (meta data) | emd-34947-v30.xml emd-34947.xml | 25.1 KB 25.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34947_fsc.xml | 12 KB | Display | FSC data file |
Images | emd_34947.png | 29.4 KB | ||
Filedesc metadata | emd-34947.cif.gz | 7 KB | ||
Others | emd_34947_half_map_1.map.gz emd_34947_half_map_2.map.gz | 165 MB 165 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34947 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34947 | HTTPS FTP |
-Related structure data
Related structure data | 8hqcMC 8hptC 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_34947.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Full map corresponding to C5a-C5aR1-Go | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.94756 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map B corresponding to C5a-C5aR1-Go
File | emd_34947_half_map_1.map | ||||||||||||
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Annotation | Half map B corresponding to C5a-C5aR1-Go | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A corresponding to C5a-C5aR1-Go
File | emd_34947_half_map_2.map | ||||||||||||
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Annotation | Half map A corresponding to C5a-C5aR1-Go | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : GPCR-G protein in complex with a natural peptide agonist
+Supramolecule #1: GPCR-G protein in complex with a natural peptide agonist
+Supramolecule #2: C5a anaphylatoxin chemotactic receptor 1
+Supramolecule #3: Guanine nucleotide-binding protein G(o) subunit alpha
+Supramolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
+Supramolecule #5: C5a anaphylatoxin
+Supramolecule #6: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
+Supramolecule #7: Antibody fragment
+Macromolecule #1: C5a anaphylatoxin chemotactic receptor 1
+Macromolecule #2: Guanine nucleotide-binding protein G(o) subunit alpha
+Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
+Macromolecule #4: C5a anaphylatoxin
+Macromolecule #5: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
+Macromolecule #6: Antibody fragment
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 42.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-8hqc: |