+Open data
-Basic information
Entry | Database: PDB / ID: 1qsj | ||||||
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Title | N-TERMINALLY TRUNCATED C3DG FRAGMENT | ||||||
Components | COMPLEMENT C3 PRECURSOR | ||||||
Keywords | IMMUNE SYSTEM / ALPHA-ALPHA BARREL | ||||||
Function / homology | Function and homology information Alternative complement activation / Activation of C3 and C5 / Regulation of Complement cascade / tolerance induction / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / vascular associated smooth muscle cell differentiation / Peptide ligand-binding receptors / oviduct epithelium development ...Alternative complement activation / Activation of C3 and C5 / Regulation of Complement cascade / tolerance induction / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / vascular associated smooth muscle cell differentiation / Peptide ligand-binding receptors / 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 / positive regulation of lipid storage / positive regulation of developmental growth / positive regulation of phagocytosis, engulfment / positive regulation of G protein-coupled receptor signaling pathway / complement receptor mediated signaling pathway / positive regulation of type IIa hypersensitivity / positive regulation of glucose transmembrane transport / complement-dependent cytotoxicity / complement activation, alternative pathway / complement activation / G alpha (i) signalling events / Neutrophil degranulation / endopeptidase inhibitor activity / neuron remodeling / amyloid-beta clearance / response to magnesium ion / positive regulation of vascular endothelial growth factor production / positive regulation of phagocytosis / response to glucocorticoid / complement activation, classical pathway / fatty acid metabolic process / response to progesterone / response to bacterium / positive regulation of receptor-mediated endocytosis / response to estrogen / positive regulation of angiogenesis / chemotaxis / response to estradiol / retina development in camera-type eye / positive regulation of ERK1 and ERK2 cascade / response to xenobiotic stimulus / inflammatory response / positive regulation of protein phosphorylation / lipid binding / cell surface / protein-containing complex / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å | ||||||
Authors | Zanotti, G. / Bassetto, A. / Battistutta, R. / Stoppini, M. / Folli, C. / Berni, R. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2000 Title: Structure at 1.44 A resolution of an N-terminally truncated form of the rat serum complement C3d fragment. Authors: Zanotti, G. / Bassetto, A. / Battistutta, R. / Folli, C. / Arcidiaco, P. / Stoppini, M. / Berni, R. #1: Journal: Science / Year: 1998 Title: X-ray Crystal Structure of C3d: A C3 Fragment and Ligand for Complement Receptor 2 Authors: Nagar, B. / Jones, R.G. / Diefenbach, R.J. / Isenman, D.E. / Rini, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qsj.cif.gz | 221.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qsj.ent.gz | 186.7 KB | Display | PDB format |
PDBx/mmJSON format | 1qsj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qs/1qsj ftp://data.pdbj.org/pub/pdb/validation_reports/qs/1qsj | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31151.398 Da / Num. of mol.: 4 / Fragment: N-TERMINALLY TRUNCATED C3DG FRAGMENT / Mutation: M1081Y, W1082V, S1085V / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Organ: PLASMA / References: UniProt: P01026 #2: 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: 2.29 Å3/Da / Density % sol: 46.37 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 25%-30% PEG 6000, 0.05 M POTASSIUM PHOSPHATE, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K | |||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 38 % | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃Details: drop consists of equal volume of protein and reservoir solutions | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 16, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→55 Å / Num. all: 64362 / Num. obs: 64362 / % possible obs: 76 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.94→2.17 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.083 / % possible all: 77.1 |
Reflection shell | *PLUS % possible obs: 77.1 % / Num. unique obs: 18274 / Mean I/σ(I) obs: 8.3 |
-Processing
Software |
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Refinement | Resolution: 1.9→55 Å / σ(F): 4 / σ(I): 2 / Stereochemistry target values: ENGH & HUBER / Details: REFLECTIONS WITH FOBS<2.5 FCALC WERE EXCLUDED FROM REFINEMENT
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Refinement step | Cycle: LAST / Resolution: 1.9→55 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.217 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |