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- PDB-3v8c: Crystal structure of monoclonal human anti-rhesus D Fc IgG1 t125(... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3v8c | |||||||||
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Title | Crystal structure of monoclonal human anti-rhesus D Fc IgG1 t125(yb2/0) double mutant (H310 and H435 in K) | |||||||||
![]() | Ig gamma-1 chain C region | |||||||||
![]() | IMMUNE SYSTEM / FC IGG1 / FC-GAMMA receptor | |||||||||
Function / homology | ![]() Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding ...Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR3A-mediated IL10 synthesis / complement activation, classical pathway / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / antigen binding / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / blood microparticle / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Menez, R. / Stura, E.A. / Bourel, D. / Siberil, S. / Jorieux, S. / De Romeuf, C. / Ducancel, F. / Fridman, W.H. / Teillaud, J.L. | |||||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.1 KB | Display | ![]() |
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PDB format | ![]() | 81.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 863.6 KB | Display | ![]() |
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Full document | ![]() | 897.8 KB | Display | |
Data in XML | ![]() | 24 KB | Display | |
Data in CIF | ![]() | 31.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3v7mSC ![]() 3v95C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 23957.139 Da / Num. of mol.: 2 / Fragment: unp residues 119-330 / Mutation: H310K, H345K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Cell line (production host): EBV-TRANSFECTED B CELL CRL-1662 Production host: ![]() ![]() |
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-Sugars , 4 types, 15 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/MAN.gif)
![](data/chem/img/GAL.gif)
![](data/chem/img/MAN.gif)
![](data/chem/img/GAL.gif)
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose Source method: isolated from a genetically manipulated source | ||||
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#3: Sugar | ChemComp-NAG / #5: Sugar | ChemComp-MAN / #6: Sugar | |
-Non-polymers , 2 types, 101 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.1 Details: 17% MPEG 5000; 21.5% ETHYLENE GLYCOL, 0.1M SODIUM CACODYLATE, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 9, 2005 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.769→45 Å / Num. all: 14583 / Num. obs: 14467 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.139 / Rsym value: 0.138 / Net I/σ(I): 15.94 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3V7M Resolution: 2.77→42.03 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.85 / SU B: 19.921 / SU ML: 0.398 / Cross valid method: THROUGHOUT / ESU R Free: 0.46 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.56 Å2
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Refinement step | Cycle: LAST / Resolution: 2.77→42.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.773→2.845 Å / Total num. of bins used: 20
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