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Yorodumi- EMDB-33891: Cryo-EM structure of the human chemerin receptor 1 complex with t... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33891 | |||||||||
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Title | Cryo-EM structure of the human chemerin receptor 1 complex with the C-terminal nonapeptide of chemerin | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information adipokinetic hormone binding / adipokinetic hormone receptor activity / platelet dense granule lumen / complement receptor activity / regulation of lipid catabolic process / antifungal innate immune response / chemokine receptor activity / embryonic digestive tract development / Class A/1 (Rhodopsin-like receptors) / antifungal humoral response ...adipokinetic hormone binding / adipokinetic hormone receptor activity / platelet dense granule lumen / complement receptor activity / regulation of lipid catabolic process / antifungal innate immune response / chemokine receptor activity / embryonic digestive tract development / Class A/1 (Rhodopsin-like receptors) / antifungal humoral response / complement receptor mediated signaling pathway / positive regulation of chemotaxis / negative regulation of interleukin-12 production / retinoid metabolic process / negative regulation of NF-kappaB transcription factor activity / positive regulation of macrophage chemotaxis / Adenylate cyclase inhibitory pathway / positive regulation of fat cell differentiation / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / regulation of calcium-mediated signaling / regulation of mitotic spindle organization / cellular response to forskolin / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / extracellular matrix / skeletal system development / Regulation of insulin secretion / G protein-coupled receptor binding / G protein-coupled receptor activity / 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 / response to peptide hormone / 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 / 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 / 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 / GDP binding / chemotaxis / G-protein beta-subunit binding / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / Platelet degranulation / insulin receptor signaling pathway / GTPase binding / retina development in camera-type eye / phospholipase C-activating G protein-coupled receptor signaling pathway / Ca2+ pathway / signaling receptor activity / positive regulation of cold-induced thermogenesis / cell cortex / midbody / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / collagen-containing extracellular matrix / defense response to Gram-negative bacterium / cell population proliferation / Ras protein signal transduction / Extra-nuclear estrogen signaling / cell differentiation / defense response to Gram-positive bacterium / inflammatory response / cell cycle / positive regulation of protein phosphorylation / immune response Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Vicugna pacos (alpaca) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.81 Å | |||||||||
Authors | Chen G / Liao Q / Ye RD / Wang J | |||||||||
Funding support | 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: Cryo-EM structure of the human chemerin receptor 1-Gi protein complex bound to the C-terminal nonapeptide of chemerin. Authors: Junlin Wang / Geng Chen / Qiwen Liao / Wenping Lyu / Aijun Liu / Lizhe Zhu / Yang Du / Richard D Ye / Abstract: Chemerin is a processed protein that acts on G protein-coupled receptors (GPCRs) for its chemotactic and adipokine activities. The biologically active chemerin (chemerin 21-157) results from ...Chemerin is a processed protein that acts on G protein-coupled receptors (GPCRs) for its chemotactic and adipokine activities. The biologically active chemerin (chemerin 21-157) results from proteolytic cleavage of prochemerin and uses its C-terminal peptide containing the sequence YFPGQFAFS for receptor activation. Here we report a high-resolution cryo-electron microscopy (cryo-EM) structure of human chemerin receptor 1 (CMKLR1) bound to the C-terminal nonapeptide of chemokine (C9) in complex with Gi proteins. C9 inserts its C terminus into the binding pocket and is stabilized through hydrophobic interactions involving its Y1, F2, F6, and F8, as well as polar interactions between G4, S9, and several amino acids lining the binding pocket of CMKLR1. Microsecond scale molecular dynamics simulations support a balanced force distribution across the whole ligand-receptor interface that enhances thermodynamic stability of the captured binding pose of C9. The C9 interaction with CMKLR1 is drastically different from chemokine recognition by chemokine receptors, which follow a two-site two-step model. In contrast, C9 takes an "S"-shaped pose in the binding pocket of CMKLR1 much like angiotensin II in the AT1 receptor. Our mutagenesis and functional analyses confirmed the cryo-EM structure and key residues in the binding pocket for these interactions. Our findings provide a structural basis for chemerin recognition by CMKLR1 for the established chemotactic and adipokine activities. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33891.map.gz | 64.3 MB | EMDB map data format | |
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Header (meta data) | emd-33891-v30.xml emd-33891.xml | 22.3 KB 22.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33891_fsc.xml | 11 KB | Display | FSC data file |
Images | emd_33891.png | 73.7 KB | ||
Others | emd_33891_half_map_1.map.gz emd_33891_half_map_2.map.gz | 115.9 MB 115.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33891 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33891 | HTTPS FTP |
-Validation report
Summary document | emd_33891_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_33891_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_33891_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | emd_33891_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33891 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33891 | HTTPS FTP |
-Related structure data
Related structure data | 7ykdMC 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_33891.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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
-Half map: #2
File | emd_33891_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33891_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : CMKLR1-Gi -scFv16 complex
+Supramolecule #1: CMKLR1-Gi -scFv16 complex
+Supramolecule #2: Retinoic acid receptor responder protein 2
+Supramolecule #3: Chemerin-like receptor 1, Guanine nucleotide-binding protein G(i)...
+Supramolecule #4: scFV16
+Macromolecule #1: Retinoic acid receptor responder protein 2
+Macromolecule #2: Chemerin-like receptor 1
+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: scFV16
+Macromolecule #7: CHOLESTEROL
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.13 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: 2.0 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |