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Yorodumi- EMDB-31962: The structure of Formyl Peptide Receptor 1 in complex with Gi and... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31962 | |||||||||
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Title | The structure of Formyl Peptide Receptor 1 in complex with Gi and peptide agonist fMIFL | |||||||||
Map data | ||||||||||
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Function / homology | Function and homology information N-formyl peptide receptor activity / complement receptor activity / scavenger receptor binding / RAGE receptor binding / complement receptor mediated signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / azurophil granule membrane / Interleukin-10 signaling / ficolin-1-rich granule membrane / T cell migration ...N-formyl peptide receptor activity / complement receptor activity / scavenger receptor binding / RAGE receptor binding / complement receptor mediated signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / azurophil granule membrane / Interleukin-10 signaling / ficolin-1-rich granule membrane / T cell migration / D2 dopamine receptor binding / Adenylate cyclase inhibitory pathway / nitric oxide mediated signal transduction / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / G protein-coupled serotonin receptor binding / cellular response to forskolin / regulation of mitotic spindle organization / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / secretory granule membrane / Regulation of insulin secretion / G protein-coupled receptor binding / G protein-coupled receptor activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Olfactory Signaling Pathway / Activation of the phototransduction cascade / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / Glucagon signaling in metabolic regulation / G protein-coupled acetylcholine receptor signaling pathway / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G beta:gamma signalling through CDC42 / response to peptide hormone / Vasopressin regulates renal water homeostasis via Aquaporins / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Glucagon-type ligand receptors / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / G alpha (z) signalling events / Adrenaline,noradrenaline inhibits insulin secretion / 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 / adenylate cyclase-activating dopamine receptor signaling pathway / G beta:gamma signalling through PI3Kgamma / GPER1 signaling / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / chemotaxis / GDP binding / cellular response to prostaglandin E stimulus / Inactivation, recovery and regulation of the phototransduction cascade / G-protein beta-subunit binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Thrombin signalling through proteinase activated receptors (PARs) / GTPase binding / retina development in camera-type eye / Ca2+ pathway / cell cortex / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / midbody / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / inflammatory response / G protein-coupled receptor signaling pathway / lysosomal membrane / cell division / GTPase activity / centrosome / Neutrophil degranulation / synapse / GTP binding / protein-containing complex binding / nucleolus / magnesium ion binding / signal transduction / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Mus musculus (house mouse) / Staphylococcus aureus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Wang XK / Chen G / Liao QW / Du Y / Hu HL / Ye DQ | |||||||||
Funding support | 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis for recognition of N-formyl peptides as pathogen-associated molecular patterns. Authors: Geng Chen / Xiankun Wang / Qiwen Liao / Yunjun Ge / Haizhan Jiao / Qiang Chen / Yezhou Liu / Wenping Lyu / Lizhe Zhu / Gydo C P van Zundert / Michael J Robertson / Georgios Skiniotis / Yang ...Authors: Geng Chen / Xiankun Wang / Qiwen Liao / Yunjun Ge / Haizhan Jiao / Qiang Chen / Yezhou Liu / Wenping Lyu / Lizhe Zhu / Gydo C P van Zundert / Michael J Robertson / Georgios Skiniotis / Yang Du / Hongli Hu / Richard D Ye / Abstract: The formyl peptide receptor 1 (FPR1) is primarily responsible for detection of short peptides bearing N-formylated methionine (fMet) that are characteristic of protein synthesis in bacteria and ...The formyl peptide receptor 1 (FPR1) is primarily responsible for detection of short peptides bearing N-formylated methionine (fMet) that are characteristic of protein synthesis in bacteria and mitochondria. As a result, FPR1 is critical to phagocyte migration and activation in bacterial infection, tissue injury and inflammation. How FPR1 distinguishes between formyl peptides and non-formyl peptides remains elusive. Here we report cryo-EM structures of human FPR1-Gi protein complex bound to S. aureus-derived peptide fMet-Ile-Phe-Leu (fMIFL) and E. coli-derived peptide fMet-Leu-Phe (fMLF). Both structures of FPR1 adopt an active conformation and exhibit a binding pocket containing the R201XXXR205 (RGIIR) motif for formyl group interaction and receptor activation. This motif works together with D106 for hydrogen bond formation with the N-formyl group and with fMet, a model supported by MD simulation and functional assays of mutant receptors with key residues for recognition substituted by alanine. The cryo-EM model of agonist-bound FPR1 provides a structural basis for recognition of bacteria-derived chemotactic peptides with potential applications in developing FPR1-targeting agents. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_31962.map.gz | 59.6 MB | EMDB map data format | |
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Header (meta data) | emd-31962-v30.xml emd-31962.xml | 23.8 KB 23.8 KB | Display Display | EMDB header |
Images | emd_31962.png | 37.5 KB | ||
Others | emd_31962_half_map_1.map.gz emd_31962_half_map_2.map.gz | 58.9 MB 59 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31962 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31962 | HTTPS FTP |
-Validation report
Summary document | emd_31962_validation.pdf.gz | 826 KB | Display | EMDB validaton report |
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Full document | emd_31962_full_validation.pdf.gz | 825.5 KB | Display | |
Data in XML | emd_31962_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | emd_31962_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31962 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31962 | HTTPS FTP |
-Related structure data
Related structure data | 7vfxMC 7euoC 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_31962.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_31962_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_31962_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Complex of FPR1 with Gi and peptide agonist fMIFL
+Supramolecule #1: Complex of FPR1 with Gi and peptide agonist fMIFL
+Supramolecule #2: FPR1 with Gi
+Supramolecule #3: peptide agonist fMIFL
+Macromolecule #1: fMet-Leu-Phe receptor
+Macromolecule #2: Guanine nucleotide-binding protein G(i) subunit alpha-1
+Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
+Macromolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
+Macromolecule #5: scFv16
+Macromolecule #6: Peptide agonist fMIFL
+Macromolecule #7: CHOLESTEROL
+Macromolecule #8: PALMITIC ACID
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 6 mg/mL |
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Buffer | pH: 7.5 |
Grid | Material: NICKEL/TITANIUM / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec. |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 49.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 105000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 171338 |
Initial angle assignment | Type: RANDOM ASSIGNMENT / Software - Name: RELION |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION |