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Yorodumi- PDB-3v7m: Crystal structure of monoclonal human anti-Rhesus D Fc IgG1 T125(... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3v7m | |||||||||
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Title | Crystal structure of monoclonal human anti-Rhesus D Fc IgG1 T125(YB2/0) in the presence of Zn2+ | |||||||||
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 / IgG immunoglobulin complex / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding ...complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / IgG immunoglobulin complex / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / FCGR3A-mediated IL10 synthesis / antigen binding / 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 / adaptive immune response / blood microparticle / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | |||||||||
Authors | Menez, R. / Stura, E.A. / 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3v7m.cif.gz | 65.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v7m.ent.gz | 46.3 KB | Display | PDB format |
PDBx/mmJSON format | 3v7m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/3v7m ftp://data.pdbj.org/pub/pdb/validation_reports/v7/3v7m | HTTPS FTP |
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-Related structure data
Related structure data | 3v8cC 3v95C 2j6eS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 23691.725 Da / Num. of mol.: 1 / Fragment: unp residues 119-327 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PCI-NEO / Cell line (production host): (ATCC, CRL-1662) [T125(YB2/0)] / Production host: Rattus norvegicus (Norway rat) / References: UniProt: P01857 |
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#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-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]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 |
-Non-polymers , 4 types, 149 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.46 % |
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Crystal grow | Temperature: 316 K / pH: 5.1 Details: 8% MPEG 5000, 300 MICRO-M ZNCL2, 100 MICRO-M NICL2, 0.1 M SODIUM CACODYLATE, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 316KK |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 19, 2003 / 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: 2.02→45 Å / Num. obs: 17681 / % possible obs: 93.2 % / Observed criterion σ(I): -2 / Redundancy: 7.2 % / Biso Wilson estimate: 47.34 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.059 / Net I/σ(I): 18.81 |
Reflection shell | Resolution: 2.02→2.14 Å / Redundancy: 6.62 % / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 2.71 / Rsym value: 0.712 / % possible all: 70.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2J6E FC PORTION ONLY. Resolution: 2.02→40.24 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / SU B: 5.625 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.222 / ESU R Free: 0.199 / 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: 47.93 Å2
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Refinement step | Cycle: LAST / Resolution: 2.02→40.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.02→2.07 Å / Total num. of bins used: 20
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