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Open data
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Basic information
Entry | Database: PDB / ID: 1qqf | ||||||
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Title | N-TERMINALLY TRUNCATED C3D,G FRAGMENT OF THE COMPLEMENT SYSTEM | ||||||
![]() | PROTEIN (COMPLEMENT C3DG) | ||||||
![]() | IMMUNE SYSTEM / ALPHA-ALPHA BARREL / COMPLEMENT | ||||||
Function / homology | ![]() 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 G protein-coupled receptor signaling pathway / positive regulation of lipid storage / positive regulation of developmental growth / positive regulation of phagocytosis, engulfment / 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 / neuron remodeling / endopeptidase inhibitor activity / amyloid-beta clearance / response to magnesium ion / positive regulation of vascular endothelial growth factor production / response to glucocorticoid / positive regulation of phagocytosis / fatty acid metabolic process / complement activation, classical pathway / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zanotti, G. / Bassetto, A. / Battistutta, R. / Stoppini, M. / Berni, R. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 68.9 KB | Display | ![]() |
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PDB format | ![]() | 55.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 415.5 KB | Display | ![]() |
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Full document | ![]() | 420.5 KB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 24.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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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Details | dimer generated from the monomer of the asymmetric unit and a second monomer related to the first by a crystallographic twofold axis |
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Components
#1: Protein | Mass: 31167.398 Da / Num. of mol.: 1 / Fragment: N-TERMINALLY TRUNCATED FRAGMENT / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.06 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: 24% PEG 6000, K PHOSPHATE 50 MM, pH 7.0 | |||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 38 % | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ / pH: 7.4 / Method: vapor diffusion, sitting dropDetails: 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: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→26.9 Å / Num. obs: 50041 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 8.04 |
Reflection shell | Resolution: 1.45→1.62 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.285 / % possible all: 97.2 |
Reflection shell | *PLUS % possible obs: 97.2 % / Num. unique obs: 13685 / Mean I/σ(I) obs: 2.6 |
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Processing
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Refinement | Resolution: 1.45→10 Å / σ(F): 4 / Stereochemistry target values: Engh & Huber / Details: ANISOTROPIC B FACTORS IN THE LAST CYCLES
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Refinement step | Cycle: LAST / Resolution: 1.45→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.212 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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