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Yorodumi- EMDB-26208: Human Amylin3 Receptor in complex with Gs and rat amylin peptide -
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Open data
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Basic information
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| Title | Human Amylin3 Receptor in complex with Gs and rat amylin peptide | ||||||||||||||||||||||||
Map data | post-processed consensus map | ||||||||||||||||||||||||
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Keywords | Amylin receptor / GPCR / RAMP3 / rat amylin / MEMBRANE PROTEIN | ||||||||||||||||||||||||
| Function / homology | Function and homology informationCalcitonin-like ligand receptors / cross-receptor inhibition within G protein-coupled receptor heterodimer / G protein-coupled receptor signaling pathway involved in heart process / adrenomedullin receptor activity / adrenomedullin receptor complex / adrenomedullin receptor signaling pathway / calcitonin binding / calcitonin family receptor activity / amylin receptor complex 1 / amylin receptor complex 2 ...Calcitonin-like ligand receptors / cross-receptor inhibition within G protein-coupled receptor heterodimer / G protein-coupled receptor signaling pathway involved in heart process / adrenomedullin receptor activity / adrenomedullin receptor complex / adrenomedullin receptor signaling pathway / calcitonin binding / calcitonin family receptor activity / amylin receptor complex 1 / amylin receptor complex 2 / calcitonin family receptor signaling pathway / amylin receptor complex 3 / amylin receptor activity / calcitonin receptor activity / calcitonin gene-related peptide receptor signaling pathway / calcitonin gene-related peptide receptor activity / amylin receptor 3 signaling pathway / amylin receptor 2 signaling pathway / amylin receptor 1 signaling pathway / amylin receptor signaling pathway / Calcitonin-like ligand receptors / negative regulation of ossification / negative regulation of bone resorption / eating behavior / negative regulation of osteoclast differentiation / response to amyloid-beta / positive regulation of cAMP/PKA signal transduction / positive regulation of receptor recycling / PKA activation in glucagon signalling / developmental growth / hair follicle placode formation / bone resorption / D1 dopamine receptor binding / intracellular transport / vascular endothelial cell response to laminar fluid shear stress / renal water homeostasis / activation of adenylate cyclase activity / Hedgehog 'off' state / cellular response to hormone stimulus / coreceptor activity / adenylate cyclase-activating adrenergic receptor signaling pathway / regulation of mRNA stability / sensory perception of pain / regulation of insulin secretion / cellular response to glucagon stimulus / positive regulation of calcium-mediated signaling / acrosomal vesicle / ossification / osteoclast differentiation / response to glucocorticoid / secretory granule / adenylate cyclase activator activity / trans-Golgi network membrane / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / intracellular protein transport / negative regulation of inflammatory response to antigenic stimulus / cellular response to estradiol stimulus / hormone activity / bone development / receptor internalization / platelet aggregation / cognition / G-protein beta/gamma-subunit complex binding / glucose metabolic process / Olfactory Signaling Pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / G beta:gamma signalling through CDC42 / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / ADP signalling through P2Y purinoceptor 12 / photoreceptor disc membrane / Sensory perception of sweet, bitter, and umami (glutamate) taste / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / sensory perception of smell / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (z) signalling events / calcium ion transport / ADP signalling through P2Y purinoceptor 1 / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / 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 / G-protein beta-subunit binding / cellular response to prostaglandin E stimulus / heterotrimeric G-protein complex Similarity search - Function | ||||||||||||||||||||||||
| Biological species | Homo sapiens (human) / ![]() ![]() | ||||||||||||||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.4 Å | ||||||||||||||||||||||||
Authors | Cao J / Belousoff MJ | ||||||||||||||||||||||||
| Funding support | Australia, Japan, 7 items
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Citation | Journal: Science / Year: 2022Title: A structural basis for amylin receptor phenotype. Authors: Jianjun Cao / Matthew J Belousoff / Yi-Lynn Liang / Rachel M Johnson / Tracy M Josephs / Madeleine M Fletcher / Arthur Christopoulos / Debbie L Hay / Radostin Danev / Denise Wootten / Patrick M Sexton / ![]() Abstract: Amylin receptors (AMYRs) are heterodimers of the calcitonin (CT) receptor (CTR) and one of three receptor activity-modifying proteins (RAMPs), AMYR, AMYR, and AMYR. Selective AMYR agonists and dual ...Amylin receptors (AMYRs) are heterodimers of the calcitonin (CT) receptor (CTR) and one of three receptor activity-modifying proteins (RAMPs), AMYR, AMYR, and AMYR. Selective AMYR agonists and dual AMYR/CTR agonists are being developed as obesity treatments; however, the molecular basis for peptide binding and selectivity is unknown. We determined the structure and dynamics of active AMYRs with amylin, AMYR with salmon CT (sCT), AMYR with sCT or human CT (hCT), and CTR with amylin, sCT, or hCT. The conformation of amylin-bound complexes was similar for all AMYRs, constrained by the RAMP, and an ordered midpeptide motif that we call the bypass motif. The CT-bound AMYR complexes were distinct, overlapping the CT-bound CTR complexes. Our findings indicate that activation of AMYRs by CT-based peptides is distinct from their activation by amylin-based peptides. This has important implications for the development of AMYR therapeutics. | ||||||||||||||||||||||||
| History |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_26208.map.gz | 166.5 MB | EMDB map data format | |
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| Header (meta data) | emd-26208-v30.xml emd-26208.xml | 37.6 KB 37.6 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_26208_fsc.xml | 12.8 KB | Display | FSC data file |
| Images | emd_26208.png | 28.2 KB | ||
| Masks | emd_26208_msk_1.map | 178 MB | Mask map | |
| Filedesc metadata | emd-26208.cif.gz | 8.5 KB | ||
| Others | emd_26208_additional_1.map.gz emd_26208_additional_2.map.gz emd_26208_additional_3.map.gz emd_26208_additional_4.map.gz emd_26208_half_map_1.map.gz emd_26208_half_map_2.map.gz | 166.5 MB 161.7 MB 159.3 MB 141.5 MB 141.8 MB 141.8 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26208 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26208 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 7tzfMC ![]() 7tyfC ![]() 7tyhC ![]() 7tyiC ![]() 7tylC ![]() 7tynC ![]() 7tyoC ![]() 7tywC ![]() 7tyxC ![]() 7tyyC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_26208.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | post-processed consensus map | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.65 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Mask #1
| File | emd_26208_msk_1.map | ||||||||||||
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| Density Histograms |
-Additional map: the combined map that samples the consensus map...
| File | emd_26208_additional_1.map | ||||||||||||
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| Annotation | the combined map that samples the consensus map and the local refined map. | ||||||||||||
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| Density Histograms |
-Additional map: post-processed map from local refinement that focused on...
| File | emd_26208_additional_2.map | ||||||||||||
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| Annotation | post-processed map from local refinement that focused on receptor region and the map was resampled to the consensus map | ||||||||||||
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| Density Histograms |
-Additional map: unfiltered map from local refinement that focused on...
| File | emd_26208_additional_3.map | ||||||||||||
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| Annotation | unfiltered map from local refinement that focused on receptor region and the map was resampled to the consensus map | ||||||||||||
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| Density Histograms |
-Additional map: unfiltered consensus map
| File | emd_26208_additional_4.map | ||||||||||||
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| Annotation | unfiltered consensus map | ||||||||||||
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| Density Histograms |
-Half map: half map of the consensus map
| File | emd_26208_half_map_1.map | ||||||||||||
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| Annotation | half map of the consensus map | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: half map of the consensus map
| File | emd_26208_half_map_2.map | ||||||||||||
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| Annotation | half map of the consensus map | ||||||||||||
| Projections & Slices |
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| Density Histograms |
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Sample components
+Entire : Human Amylin 3 Receptor in complex with Gs and rat amylin peptide
+Supramolecule #1: Human Amylin 3 Receptor in complex with Gs and rat amylin peptide
+Macromolecule #1: Receptor activity-modifying protein 3
+Macromolecule #2: amylin peptide
+Macromolecule #3: Calcitonin receptor
+Macromolecule #4: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
+Macromolecule #5: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
+Macromolecule #6: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
+Macromolecule #7: nanobody 35
+Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #9: (2S)-2-{[(1R)-1-hydroxyhexadecyl]oxy}-3-{[(1R)-1-hydroxyoctadecyl...
+Macromolecule #10: PALMITIC ACID
+Macromolecule #11: CHOLESTEROL HEMISUCCINATE
+Macromolecule #12: water
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Concentration | 4 mg/mL |
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| Buffer | pH: 7.4 |
| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.8 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: 1.5 µm / Nominal defocus min: 0.5 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Homo sapiens (human)
Authors
Australia,
Japan, 7 items
Citation






































Z (Sec.)
Y (Row.)
X (Col.)












































































Trichoplusia ni (cabbage looper)





Processing
FIELD EMISSION GUN

