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Yorodumi- PDB-4cdh: Crystallographic structure of the Human Igg1 alpha 2-6 sialilated... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cdh | |||||||||
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Title | Crystallographic structure of the Human Igg1 alpha 2-6 sialilated Fc-Fragment | |||||||||
Components | IG GAMMA-1 CHAIN C REGION | |||||||||
Keywords | IMMUNE SYSTEM / C-LECTIN CRD / SIGN-R1 / INMUNE SYSTEM / CAPSULAR POLYSACCHARIDE | |||||||||
Function / homology | Function and homology information complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis ...complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis / complement activation, classical pathway / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / blood microparticle / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.3 Å | |||||||||
Authors | Silva-Martin, N. / Bartual, S.G. / Hermoso, J.A. | |||||||||
Citation | Journal: Structure / Year: 2014 Title: Structural Basis for Selective Recognition of Endogenous and Microbial Polysaccharides by Macrophage Receptor Sign-R1 Authors: Silva-Martin, N. / Bartual, S.G. / Rodriguez, A. / Ramirez, E. / Chacon, P. / Anthony, R.M. / Park, C.G. / Hermoso, J.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cdh.cif.gz | 99.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cdh.ent.gz | 80.1 KB | Display | PDB format |
PDBx/mmJSON format | 4cdh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/4cdh ftp://data.pdbj.org/pub/pdb/validation_reports/cd/4cdh | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28361.252 Da / Num. of mol.: 2 / Fragment: FC, RESIDUES 101-330 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P01857 #2: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-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: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.06 % / Description: NONE |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: CRYSTALLIZATION TRIALS WERE PERFORMED AT 18 C BY THE SITTING DROP VAPOUR DIFFUSION METHOD. CRYSTALS GROWN BY MIXING 1 UL OF FC-SIAL (9 MG/ML IN PBS) WITH 3 UL OF PRECIPITANT SOLUTION ...Details: CRYSTALLIZATION TRIALS WERE PERFORMED AT 18 C BY THE SITTING DROP VAPOUR DIFFUSION METHOD. CRYSTALS GROWN BY MIXING 1 UL OF FC-SIAL (9 MG/ML IN PBS) WITH 3 UL OF PRECIPITANT SOLUTION CONSISTING OF 0.1M HEPES PH7, 16% PEG 6000, VAPOR DIFFUSION, TEMPERATURE 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Type: ESRF / Wavelength: 0.99 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20.1 Å / Num. obs: 24279 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.7 |
-Processing
Software | Name: REFMAC / Version: 5.7.0029 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.3→20.1 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.887 / SU B: 8.002 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.333 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.124 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20.1 Å
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