+Open data
-Basic information
Entry | Database: PDB / ID: 3g6j | ||||||
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Title | C3b in complex with a C3b specific Fab | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Complement / C3b / Fab / Antibody:Antigen / Age-related macular degeneration / Cleavage on pair of basic residues / Complement alternate pathway / Complement pathway / Disease mutation / Glycoprotein / Immune response / Inflammatory response / Innate immunity / Phosphoprotein / Secreted / Thioester bond | ||||||
Function / homology | Function and homology information oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway ...oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of phagocytosis, engulfment / complement receptor mediated signaling pathway / Activation of C3 and C5 / positive regulation of type IIa hypersensitivity / positive regulation of glucose transmembrane transport / complement-dependent cytotoxicity / complement activation, alternative pathway / complement activation / neuron remodeling / endopeptidase inhibitor activity / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production / Purinergic signaling in leishmaniasis infection / complement activation, classical pathway / Peptide ligand-binding receptors / fatty acid metabolic process / Regulation of Complement cascade / Post-translational protein phosphorylation / response to bacterium / positive regulation of receptor-mediated endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / G alpha (i) signalling events / blood microparticle / secretory granule lumen / immune response / inflammatory response / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Wiesmann, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Structural and Functional Analysis of a C3b-specific Antibody That Selectively Inhibits the Alternative Pathway of Complement Authors: Katschke, K.J. / Stawicki, S. / Yin, J. / Steffek, M. / Xi, H. / Sturgeon, L. / Hass, P.E. / Loyet, K.M. / Deforge, L. / Wu, Y. / van Lookeren Campagne, M. / Wiesmann, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g6j.cif.gz | 768.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g6j.ent.gz | 620.8 KB | Display | PDB format |
PDBx/mmJSON format | 3g6j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g6/3g6j ftp://data.pdbj.org/pub/pdb/validation_reports/g6/3g6j | HTTPS FTP |
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-Related structure data
Related structure data | 2icfS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 71322.242 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024 #2: Protein | Mass: 104073.164 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024 #3: Antibody | Mass: 23345.873 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #4: Antibody | Mass: 23793.562 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #5: Chemical | |
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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: 2.93 Å3/Da / Density % sol: 58.09 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.8 Details: Crystals of the C3b:S77 complex were obtained within a week at 19\xB0 C from 4 ml hanging drops, consisting of a 1:1 ratio of protein solution (10 mg/ml protein in 50 mM NaCl, 25 mM TRIS pH ...Details: Crystals of the C3b:S77 complex were obtained within a week at 19\xB0 C from 4 ml hanging drops, consisting of a 1:1 ratio of protein solution (10 mg/ml protein in 50 mM NaCl, 25 mM TRIS pH 7.8) to mother liquor (10% PEG 4000, 0.2 M MgCl2, 100 mM Na-HEPES, pH 7.0), suspended over mother liquor, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 8, 2007 / Details: mirrors |
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→50 Å / Num. all: 101495 / Num. obs: 101590 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.0135 |
Reflection shell | Resolution: 3.05→3.16 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 10108 / Rsym value: 0.667 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2ICF Resolution: 3.1→20 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.829 / SU B: 49.527 / SU ML: 0.401 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.518 / 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: 35.199 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.162 Å / Total num. of bins used: 25
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Refinement TLS params. | Method: refined / Origin x: -47.5365 Å / Origin y: 19.9956 Å / Origin z: -34.7955 Å
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Refinement TLS group |
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