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Yorodumi- EMDB-26178: Human Amylin1 Receptor in complex with Gs and rat amylin peptide -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26178 | ||||||||||||||||||||||||
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Title | Human Amylin1 Receptor in complex with Gs and rat amylin peptide | ||||||||||||||||||||||||
Map data | Post-processed consensus map | ||||||||||||||||||||||||
Sample |
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Keywords | Amylin receptor / GPCR / RAMP / MEMBRANE PROTEIN | ||||||||||||||||||||||||
Function / homology | Function and homology information Calcitonin-like ligand receptors / calcitonin gene-related peptide binding / CGRP receptor complex / calcitonin gene-related peptide receptor signaling pathway / calcitonin binding / amylin receptor complex 1 / amylin receptor complex 2 / positive regulation of protein glycosylation / cross-receptor inhibition within G protein-coupled receptor heterodimer / amylin receptor complex 3 ...Calcitonin-like ligand receptors / calcitonin gene-related peptide binding / CGRP receptor complex / calcitonin gene-related peptide receptor signaling pathway / calcitonin binding / amylin receptor complex 1 / amylin receptor complex 2 / positive regulation of protein glycosylation / cross-receptor inhibition within G protein-coupled receptor heterodimer / amylin receptor complex 3 / amylin receptor activity / calcitonin receptor activity / calcitonin gene-related peptide receptor activity / amylin receptor signaling pathway / positive regulation of adenylate cyclase activity / Calcitonin-like ligand receptors / regulation of G protein-coupled receptor signaling pathway / negative regulation of ossification / negative regulation of bone resorption / eating behavior / positive regulation of protein kinase A signaling / negative regulation of osteoclast differentiation / response to amyloid-beta / PKA activation in glucagon signalling / hair follicle placode formation / developmental growth / D1 dopamine receptor binding / intracellular transport / renal water homeostasis / bone resorption / Hedgehog 'off' state / coreceptor activity / adenylate cyclase-activating adrenergic receptor signaling pathway / activation of adenylate cyclase activity / response to glucocorticoid / cellular response to hormone stimulus / cellular response to glucagon stimulus / regulation of mRNA stability / sensory perception of pain / adenylate cyclase activator activity / regulation of insulin secretion / positive regulation of calcium-mediated signaling / ossification / osteoclast differentiation / acrosomal vesicle / trans-Golgi network membrane / secretory granule / protein localization to plasma membrane / negative regulation of inflammatory response to antigenic stimulus / intracellular protein transport / bone development / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / adenylate cyclase-activating G protein-coupled receptor signaling pathway / receptor internalization / hormone activity / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / cilium / G protein-coupled acetylcholine receptor signaling pathway / G protein activity / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / platelet aggregation / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / cognition / 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 / ADORA2B mediated anti-inflammatory cytokines production / cellular response to catecholamine stimulus / 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 / glucose metabolic process / calcium ion transport / GPER1 signaling / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / sensory perception of smell / G alpha (12/13) signalling events / extracellular vesicle / protein transport / signaling receptor complex adaptor activity Similarity search - Function | ||||||||||||||||||||||||
Biological species | Homo sapiens (human) / Lama glama (llama) / Rattus norvegicus (Norway rat) | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.2 Å | ||||||||||||||||||||||||
Authors | Cao J / Belousoff MJ | ||||||||||||||||||||||||
Funding support | Australia, Japan, 7 items
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Citation | Journal: Science / Year: 2022 Title: 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_26178.map.gz | 85.5 MB | EMDB map data format | |
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Header (meta data) | emd-26178-v30.xml emd-26178.xml | 32.3 KB 32.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26178_fsc.xml | 10.2 KB | Display | FSC data file |
Images | emd_26178.png | 26.5 KB | ||
Masks | emd_26178_msk_1.map | 91.1 MB | Mask map | |
Filedesc metadata | emd-26178.cif.gz | 7.6 KB | ||
Others | emd_26178_additional_1.map.gz emd_26178_additional_2.map.gz emd_26178_additional_3.map.gz emd_26178_half_map_1.map.gz emd_26178_half_map_2.map.gz | 81.5 MB 84.2 MB 71.5 MB 71.8 MB 71.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26178 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26178 | HTTPS FTP |
-Validation report
Summary document | emd_26178_validation.pdf.gz | 856.2 KB | Display | EMDB validaton report |
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Full document | emd_26178_full_validation.pdf.gz | 855.7 KB | Display | |
Data in XML | emd_26178_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | emd_26178_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26178 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26178 | HTTPS FTP |
-Related structure data
Related structure data | 7tyfMC 7tyhC 7tyiC 7tylC 7tynC 7tyoC 7tywC 7tyxC 7tyyC 7tzfC 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_26178.map.gz / Format: CCP4 / Size: 91.1 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: 0.83 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_26178_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Locally Refined unfiltered map focussed on receptor
File | emd_26178_additional_1.map | ||||||||||||
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Annotation | Locally Refined unfiltered map focussed on receptor | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Locallly refined post-processed map focussed on receptor.
File | emd_26178_additional_2.map | ||||||||||||
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Annotation | Locallly refined post-processed map focussed on receptor. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Unfiltered consensus map
File | emd_26178_additional_3.map | ||||||||||||
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Annotation | Unfiltered consensus map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_26178_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_26178_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Human Amylin1 Receptor in complex with Gs and rat amylin peptide
+Supramolecule #1: Human Amylin1 Receptor in complex with Gs and rat amylin peptide
+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: Receptor activity-modifying protein 1
+Macromolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
+Macromolecule #5: Nanobody 35
+Macromolecule #6: amylin peptide
+Macromolecule #7: Calcitonin receptor
+Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #9: PALMITIC ACID
+Macromolecule #10: CHOLESTEROL HEMISUCCINATE
+Macromolecule #11: (2S)-2-{[(1R)-1-hydroxyhexadecyl]oxy}-3-{[(1R)-1-hydroxyoctadecyl...
+Macromolecule #12: PHOSPHATIDYLETHANOLAMINE
+Macromolecule #13: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 65.3 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 |