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Yorodumi- EMDB-43877: Human Amylin1 Receptor in Complex with Gs and human Calcitonin Ge... -
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Open data
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Basic information
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| Title | Human Amylin1 Receptor in Complex with Gs and human Calcitonin Gene-Related Peptide | |||||||||||||||
Map data | postprocess consensus map | |||||||||||||||
Sample |
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Keywords | Amylin receptor / GPCR / RAMP3 / Calcitonin Gene-Related Peptide / MEMBRANE PROTEIN | |||||||||||||||
| Function / homology | Function and homology informationnervous system process involved in regulation of systemic arterial blood pressure / calcitonin gene-related peptide binding / CGRP receptor complex / 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 ...nervous system process involved in regulation of systemic arterial blood pressure / calcitonin gene-related peptide binding / CGRP receptor complex / 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 / positive regulation of glycoprotein biosynthetic process / positive regulation of interleukin-1 alpha production / amylin receptor 3 signaling pathway / amylin receptor 2 signaling pathway / negative regulation of calcium ion transport into cytosol / amylin receptor 1 signaling pathway / amylin receptor signaling pathway / positive regulation of macrophage differentiation / Calcitonin-like ligand receptors / regulation of G protein-coupled receptor signaling pathway / vasculature development / G protein-coupled receptor internalization / endothelial cell proliferation / negative regulation of ossification / negative regulation of bone resorption / leukocyte cell-cell adhesion / negative regulation of osteoclast differentiation / response to amyloid-beta / adenylate cyclase-activating G protein-coupled bile acid receptor signaling pathway / adenylate cyclase-activating serotonin receptor signaling pathway / positive regulation of cAMP/PKA signal transduction / regulation of skeletal muscle contraction / PKA activation in glucagon signalling / hair follicle placode formation / developmental growth / intracellular transport / D1 dopamine receptor binding / endothelial cell migration / regulation of cytosolic calcium ion concentration / vascular endothelial cell response to laminar fluid shear stress / renal water homeostasis / Hedgehog 'off' state / activation of adenylate cyclase activity / coreceptor activity / cellular response to hormone stimulus / cellular response to acidic pH / adenylate cyclase-activating adrenergic receptor signaling pathway / negative regulation of blood pressure / regulation of mRNA stability / cellular response to glucagon stimulus / positive regulation of calcium-mediated signaling / osteoclast differentiation / intracellular glucose homeostasis / acrosomal vesicle / ossification / response to glucocorticoid / adenylate cyclase activator activity / positive regulation of insulin secretion involved in cellular response to glucose stimulus / trans-Golgi network membrane / positive regulation of interleukin-8 production / protein localization to plasma membrane / negative regulation of inflammatory response to antigenic stimulus / response to prostaglandin E / hormone activity / intracellular protein transport / bone development / receptor internalization / platelet aggregation / vasodilation / regulation of blood pressure / cognition / G-protein beta/gamma-subunit complex binding / 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 / 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 / positive regulation of insulin secretion / 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 smell / calcium ion transport / Glucagon-type ligand receptors / Sensory perception of sweet, bitter, and umami (glutamate) taste / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (z) signalling events Similarity search - Function | |||||||||||||||
| Biological species | Homo sapiens (human) / ![]() | |||||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.4 Å | |||||||||||||||
Authors | Cao J / Belousoff MJ / Wootten DL / Sexton PM | |||||||||||||||
| Funding support | Australia, Japan, 4 items
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Citation | Journal: Biochemistry / Year: 2024Title: Cryo-EM Structure of the Human Amylin 1 Receptor in Complex with CGRP and Gs Protein. Authors: Jianjun Cao / Matthew J Belousoff / Radostin Danev / Arthur Christopoulos / Denise Wootten / Patrick M Sexton / ![]() Abstract: Inhibition of calcitonin gene-related peptide (CGRP) or its cognate CGRP receptor (CGRPR) has arisen as a major breakthrough in the treatment of migraine. However, a second CGRP-responsive receptor ...Inhibition of calcitonin gene-related peptide (CGRP) or its cognate CGRP receptor (CGRPR) has arisen as a major breakthrough in the treatment of migraine. However, a second CGRP-responsive receptor exists, the amylin (Amy) 1 receptor (AMYR), yet its involvement in the pathology of migraine is poorly understood. AMYR and CGRPR are heterodimers consisting of receptor activity-modifying protein 1 (RAMP1) with the calcitonin receptor (CTR) and the calcitonin receptor-like receptor (CLR), respectively. Here, we present the structure of AMYR in complex with CGRP and Gs protein and compare it with the reported structures of the AMYR complex with rat amylin (rAmy) and the CGRPR in complex with CGRP. Despite similar protein backbones observed within the receptors and the N- and C-termini of the two peptides bound to the AMYR complexes, they have distinct organization in the peptide midregions (the bypass motif) that is correlated with differences in the dynamics of the respective receptor extracellular domains. Moreover, divergent conformations of extracellular loop (ECL) 3, intracellular loop (ICL) 2, and ICL3 within the CTR and CLR protomers are evident when comparing the CGRP bound to the CGRPR and AMYR, which influences the binding mode of CGRP. However, the conserved interactions made by the C-terminus of CGRP to the CGRPR and AMYR are likely to account for cross-reactivity of nonpeptide CGRPR antagonists observed at AMYR, which also extends to other clinically used CGRPR blockers, including antibodies. | |||||||||||||||
| History |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_43877.map.gz | 166.1 MB | EMDB map data format | |
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| Header (meta data) | emd-43877-v30.xml emd-43877.xml | 46.5 KB 46.5 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_43877_fsc.xml | 12.8 KB | Display | FSC data file |
| Images | emd_43877.png | 18.3 KB | ||
| Masks | emd_43877_msk_1.map | 178 MB | Mask map | |
| Filedesc metadata | emd-43877.cif.gz | 9.2 KB | ||
| Others | emd_43877_additional_1.map.gz emd_43877_additional_2.map.gz emd_43877_additional_3.map.gz emd_43877_additional_4.map.gz emd_43877_additional_5.map.gz emd_43877_additional_6.map.gz emd_43877_additional_7.map.gz emd_43877_half_map_1.map.gz emd_43877_half_map_2.map.gz | 158.9 MB 152.4 MB 156.3 MB 141.1 MB 156.6 MB 155.6 MB 163.1 MB 141.5 MB 141.5 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43877 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43877 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9aucMC 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_43877.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | postprocess 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
+Additional map: postprocess map of receptor-focused refinement using auto-generated B...
+Additional map: postprocess map from the ECD-focused refinement using B-factor (-15)
+Additional map: sharpened map of receptor-focused refinement using manual input...
+Additional map: unfiltered consensus map
+Additional map: unfiltered map from the receptor-focused refinement
+Additional map: postprocess map from the ECD-focused refinement
+Additional map: postprocess map from the receptorTMD-focused refinement
+Half map: #2
+Half map: #1
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Sample components
+Entire : Human Amylin 1 Receptor in complex with Gs and human calcitonin g...
+Supramolecule #1: Human Amylin 1 Receptor in complex with Gs and human calcitonin g...
+Macromolecule #1: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
+Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
+Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
+Macromolecule #4: Nanobody 35
+Macromolecule #5: Receptor activity-modifying protein 1
+Macromolecule #6: Calcitonin gene-related peptide 1
+Macromolecule #7: Calcitonin receptor
+Macromolecule #8: PALMITIC ACID
+Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #10: CHOLESTEROL HEMISUCCINATE
+Macromolecule #11: 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 | 5.8 mg/mL |
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| Buffer | pH: 7.4 |
| Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING |
| 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) / Number grids imaged: 1 / Number real images: 7049 / Average exposure time: 16.12 sec. / Average electron dose: 71.15 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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Image processing
-Atomic model buiding 1
| Refinement | Overall B value: 41 |
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| Output model | ![]() PDB-9auc: |
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About Yorodumi



Keywords
Homo sapiens (human)
Authors
Australia,
Japan, 4 items
Citation



















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




































































































Trichoplusia ni (cabbage looper)




FIELD EMISSION GUN


