[English] 日本語
Yorodumi- PDB-3v95: Crystal structure of monoclonal human anti-rhesus D Fc and IgG1 t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3v95 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of monoclonal human anti-rhesus D Fc and IgG1 t125(yb2/0) in the presence of EDTA | |||||||||
Components | Ig gamma-1 chain C region | |||||||||
Keywords | IMMUNE SYSTEM / FC IGG1 / FC-GAMMA receptor | |||||||||
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 / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.7 Å | |||||||||
Authors | Menez, R. / A Stura, E. / Bourel, D. / Siberil, S. / Jorieux, S. / De Romeuf, C. / Ducancel, F. / Fridman, W.H. / Teillaud, J.L. | |||||||||
Citation | Journal: Immunol.Lett. / Year: 2012 Title: Effect of zinc on human IgG1 and its Fc gamma R interactions. Authors: Siberil, S. / Menez, R. / Jorieux, S. / de Romeuf, C. / Bourel, D. / Fridman, W.H. / Ducancel, F. / Stura, E.A. / Teillaud, J.L. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3v95.cif.gz | 105 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3v95.ent.gz | 80.6 KB | Display | PDB format |
PDBx/mmJSON format | 3v95.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v9/3v95 ftp://data.pdbj.org/pub/pdb/validation_reports/v9/3v95 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3v7mC 3v8cSC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 23975.072 Da / Num. of mol.: 2 / Fragment: unp residues 119-330 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Plasmid: PCI-NEO / Cell line (production host): (ATCC, CRL-1662) [T125(YB2/0)] / Production host: Rattus norvegicus (Norway rat) / References: UniProt: P01857 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.53 % |
---|---|
Crystal grow | Temperature: 293 K / pH: 5.1 Details: 12.8% MPEG 5000, 21.5% ETHYLENE GLYCOL, 0.002M EDTA, 0.1 M SODIUM CACODYLATE, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.00677 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 5, 2004 / Details: MIRRORS |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00677 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 15731 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 44.07 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.1 / Net I/σ(I): 17.56 |
Reflection shell | Resolution: 2.69→2.85 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 3.78 / Rsym value: 0.491 / % possible all: 97.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 3V8C Resolution: 2.7→41.89 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.838 / SU B: 17.32 / SU ML: 0.368 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 3.082 / ESU R Free: 0.435 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.73 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→41.89 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.69→2.76 Å / Total num. of bins used: 20
|