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Yorodumi- EMDB-31979: Neuropeptide Y Y1 Receptor (NPY1R) in Complex with G Protein and ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31979 | |||||||||
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Title | Neuropeptide Y Y1 Receptor (NPY1R) in Complex with G Protein and its endogeneous Peptide-Agonist Neuropeptide Y (NPY) | |||||||||
Map data | Merged density of NPY-Y1R-Gi-scFv16 complex generated by vop maximum | |||||||||
Sample |
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Function / homology | Function and homology information pancreatic polypeptide receptor activity / peptide YY receptor activity / neuropeptide Y receptor activity / synaptic signaling via neuropeptide / neuropeptide Y receptor binding / intestinal epithelial cell differentiation / positive regulation of appetite / neuropeptide receptor activity / adult feeding behavior / neuropeptide hormone activity ...pancreatic polypeptide receptor activity / peptide YY receptor activity / neuropeptide Y receptor activity / synaptic signaling via neuropeptide / neuropeptide Y receptor binding / intestinal epithelial cell differentiation / positive regulation of appetite / neuropeptide receptor activity / adult feeding behavior / neuropeptide hormone activity / neuropeptide binding / feeding behavior / central nervous system neuron development / outflow tract morphogenesis / neuronal dense core vesicle / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / regulation of multicellular organism growth / calcium channel regulator activity / neuropeptide signaling pathway / Adenylate cyclase inhibitory pathway / GABA-ergic synapse / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / G protein-coupled serotonin receptor binding / cellular response to forskolin / regulation of mitotic spindle organization / sensory perception of pain / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Peptide ligand-binding receptors / locomotory behavior / Regulation of insulin secretion / G protein-coupled receptor activity / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / 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 / cerebral cortex development / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / response to peptide hormone / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors / regulation of blood pressure / 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 / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / adenylate cyclase-activating dopamine receptor signaling pathway / 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 / GDP binding / glucose metabolic process / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / neuron projection development / 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 / GTPase binding / phospholipase C-activating G protein-coupled receptor signaling pathway / Ca2+ pathway / cell cortex / midbody / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / chemical synaptic transmission / cell population proliferation / Ras protein signal transduction / Extra-nuclear estrogen signaling / neuron projection / G protein-coupled receptor signaling pathway / cell cycle / lysosomal membrane / cell division Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Park C / Kim J / Jeong H / Kang H / Bang I / Choi H-J | |||||||||
Funding support | Korea, Republic Of, 2 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis of neuropeptide Y signaling through Y1 receptor. Authors: Chaehee Park / Jinuk Kim / Seung-Bum Ko / Yeol Kyo Choi / Hyeongseop Jeong / Hyeonuk Woo / Hyunook Kang / Injin Bang / Sang Ah Kim / Tae-Young Yoon / Chaok Seok / Wonpil Im / Hee-Jung Choi / Abstract: Neuropeptide Y (NPY) is highly abundant in the brain and involved in various physiological processes related to food intake and anxiety, as well as human diseases such as obesity and cancer. However, ...Neuropeptide Y (NPY) is highly abundant in the brain and involved in various physiological processes related to food intake and anxiety, as well as human diseases such as obesity and cancer. However, the molecular details of the interactions between NPY and its receptors are poorly understood. Here, we report a cryo-electron microscopy structure of the NPY-bound neuropeptide Y1 receptor (YR) in complex with G protein. The NPY C-terminal segment forming the extended conformation binds deep into the YR transmembrane core, where the amidated C-terminal residue Y36 of NPY is located at the base of the ligand-binding pocket. Furthermore, the helical region and two N-terminal residues of NPY interact with YR extracellular loops, contributing to the high affinity of NPY for YR. The structural analysis of NPY-bound YR and mutagenesis studies provide molecular insights into the activation mechanism of YR upon NPY binding. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_31979.map.gz | 229.4 MB | EMDB map data format | |
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Header (meta data) | emd-31979-v30.xml emd-31979.xml | 30.6 KB 30.6 KB | Display Display | EMDB header |
Images | emd_31979.png | 57.7 KB | ||
Others | emd_31979_additional_1.map.gz emd_31979_additional_2.map.gz emd_31979_additional_3.map.gz | 229.8 MB 229.8 MB 230.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31979 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31979 | HTTPS FTP |
-Related structure data
Related structure data | 7vgxMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_31979.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Merged density of NPY-Y1R-Gi-scFv16 complex generated by vop maximum | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.865 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Local refined density of NPY-Y1R complex
File | emd_31979_additional_1.map | ||||||||||||
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Annotation | Local refined density of NPY-Y1R complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Local refined density of Gi-scFv16 complex
File | emd_31979_additional_2.map | ||||||||||||
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Annotation | Local refined density of Gi-scFv16 complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Density of NPY-Y1R-Gi-scFv16 complex generated by non-uniform refinement...
File | emd_31979_additional_3.map | ||||||||||||
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Annotation | Density of NPY-Y1R-Gi-scFv16 complex generated by non-uniform refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Complex of Neuropeptide Y Y1 Receptor (NPY1R) with its endogeneou...
+Supramolecule #1: Complex of Neuropeptide Y Y1 Receptor (NPY1R) with its endogeneou...
+Supramolecule #2: Neuropeptide Y Y1 Receptor (NPY1R)
+Supramolecule #3: nucleotide-free G-Protein heterotrimer
+Supramolecule #4: Neuropeptide Y
+Supramolecule #5: single-chain antibody Fv fragment (scFv16)
+Macromolecule #1: Neuropeptide Y receptor type 1
+Macromolecule #2: Neuropeptide Y
+Macromolecule #3: Guanine nucleotide-binding protein G(i) subunit alpha-1
+Macromolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
+Macromolecule #5: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
+Macromolecule #6: single-chain antibody Fv fragment (scFv16)
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 11.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 285 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 5 seconds before plunging. |
-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 / Cs: 0.1 mm / Nominal defocus max: 3.75 µm / Nominal defocus min: 1.25 µm / Nominal magnification: 75000 |
Specialist optics | Spherical aberration corrector: Microscope was modified with a Cs corrector |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 1339224 |
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CTF correction | Software - Name: cryoSPARC (ver. 3.2.0) |
Startup model | Type of model: OTHER Details: Initial 3D volume generated by ab initio reconstruction was used as startup model. |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Number images used: 233117 |