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- EMDB-31962: The structure of Formyl Peptide Receptor 1 in complex with Gi and... -
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Open data
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Basic information
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Title | The structure of Formyl Peptide Receptor 1 in complex with Gi and peptide agonist fMIFL | |||||||||
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Function / homology | ![]() N-formyl peptide receptor activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Wang XK / Chen G / Liao QW / Du Y / Hu HL / Ye DQ | |||||||||
Funding support | 1 items
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![]() | ![]() 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. | |||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.8 KB 23.8 KB | Display Display | ![]() |
Images | ![]() | 37.5 KB | ||
Others | ![]() ![]() | 58.9 MB 59 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vfxMC ![]() 7euoC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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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Density Histograms |
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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 | ![]() |
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Aggregation state | particle |
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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 |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
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 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Initial angle assignment | Type: RANDOM ASSIGNMENT / Software - Name: RELION |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION |
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 |