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Yorodumi- PDB-8sm2: Crystal Structure of the macaque FcalphaRI bound to macaque IgA Fc. -
+Open data
-Basic information
Entry | Database: PDB / ID: 8sm2 | ||||||
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Title | Crystal Structure of the macaque FcalphaRI bound to macaque IgA Fc. | ||||||
Components |
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Keywords | IMMUNE SYSTEM / IGA / FCARI / FcalphaRI / CD89 / ANTIBODY / FC RECEPTOR / IMMUNOGLOBULIN-LIKE DOMAIN | ||||||
Function / homology | Function and homology information immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response Similarity search - Function | ||||||
Biological species | Macaca mulatta (Rhesus monkey) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å | ||||||
Authors | Tolbert, W.D. / Pazgier, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal Structure of the macaque FcalphaRI bound to macaque IgA Fc. Authors: Tolbert, W.D. / Pazgier, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8sm2.cif.gz | 181.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8sm2.ent.gz | 144.6 KB | Display | PDB format |
PDBx/mmJSON format | 8sm2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sm/8sm2 ftp://data.pdbj.org/pub/pdb/validation_reports/sm/8sm2 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23648.801 Da / Num. of mol.: 1 / Fragment: Fc fragment of the macaque IgA Source method: isolated from a genetically manipulated source Details: 100% match to GenBank:NP_001035039 / Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell (production host): HEK 293 GnT1- / Production host: Homo sapiens (human) / References: UniProt: H9H2V9 | ||||
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#2: Protein | Mass: 23613.494 Da / Num. of mol.: 1 / Fragment: macaque FcalphaRI (CD89) Source method: isolated from a genetically manipulated source Details: 100% match to GenBank:QJB76120 / Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: EGK_11053 / Cell (production host): HEK 293 GnT1- / Production host: Homo sapiens (human) / References: UniProt: G7NN72 | ||||
#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
#4: Sugar | ChemComp-NAG / #5: Chemical | ChemComp-SO4 / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.56 Å3/Da / Density % sol: 65.46 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100 mM ammonium sulfate 12% PEG 3350 100 mM Tris-HCl pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 5, 2022 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→50 Å / Num. obs: 12135 / % possible obs: 98 % / Redundancy: 5.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.046 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 3.15→3.2 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.819 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 481 / CC1/2: 0.54 / Rpim(I) all: 0.542 / % possible all: 81.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→28.29 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.15→28.29 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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