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Yorodumi- PDB-6xzu: Complex of C-terminal domain of murine complement C3b with the hC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xzu | ||||||
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Title | Complex of C-terminal domain of murine complement C3b with the hC3Nb3 nanobody | ||||||
Components |
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Keywords | IMMUNE SYSTEM / complex / complement / nanobody / innate immune system | ||||||
Function / homology | Function and homology information Alternative complement activation / : / Activation of C3 and C5 / Peptide ligand-binding receptors / Regulation of Complement cascade / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process ...Alternative complement activation / : / Activation of C3 and C5 / Peptide ligand-binding receptors / Regulation of Complement cascade / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / G alpha (i) signalling events / 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 / positive regulation of type IIa hypersensitivity / positive regulation of glucose transmembrane transport / complement-dependent cytotoxicity / complement activation, alternative pathway / complement activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / endopeptidase inhibitor activity / neuron remodeling / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production / positive regulation of phagocytosis / fatty acid metabolic process / Neutrophil degranulation / complement activation, classical pathway / response to bacterium / positive regulation of receptor-mediated endocytosis / positive regulation of angiogenesis / blood coagulation / positive regulation of ERK1 and ERK2 cascade / positive regulation of protein phosphorylation / inflammatory response / lipid binding / cell surface / protein-containing complex / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Lama glama (llama) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Andersen, G.R. / Pedersen, H. | ||||||
Funding support | Denmark, 1items
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Citation | Journal: J Immunol. / Year: 2020 Title: A Complement C3-Specific Nanobody for Modulation of the Alternative Cascade Identifies the C-Terminal Domain of C3b as Functional in C5 Convertase Activity. Authors: Pedersen, H. / Jensen, R.K. / Jensen, J.M.B. / Fox, R. / Pedersen, D.V. / Olesen, H.G. / Hansen, A.G. / Christiansen, D. / Mazarakis, S.M.M. / Lojek, N. / Hansen, P. / Gadeberg, T.A.F. / ...Authors: Pedersen, H. / Jensen, R.K. / Jensen, J.M.B. / Fox, R. / Pedersen, D.V. / Olesen, H.G. / Hansen, A.G. / Christiansen, D. / Mazarakis, S.M.M. / Lojek, N. / Hansen, P. / Gadeberg, T.A.F. / Zarantonello, A. / Laursen, N.S. / Mollnes, T.E. / Johnson, M.B. / Stevens, B. / Thiel, S. / Andersen, G.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xzu.cif.gz | 228.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xzu.ent.gz | 154.7 KB | Display | PDB format |
PDBx/mmJSON format | 6xzu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xzu_validation.pdf.gz | 419 KB | Display | wwPDB validaton report |
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Full document | 6xzu_full_validation.pdf.gz | 420.7 KB | Display | |
Data in XML | 6xzu_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 6xzu_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xz/6xzu ftp://data.pdbj.org/pub/pdb/validation_reports/xz/6xzu | HTTPS FTP |
-Related structure data
Related structure data | 2i07S S: Starting model for refinement |
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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
#1: Antibody | Mass: 13959.612 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Single domain nanobody selected from lama immunization library Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) |
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#2: Protein | Mass: 17177.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: From murine complement C3b / Source: (gene. exp.) Mus musculus (house mouse) / Gene: C3 / Production host: Escherichia coli (E. coli) / References: UniProt: P01027 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.16 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 17.5% PEG 4K, 33 mM NaOAc (pH 4.3), 66 mM NaOAc (pH 5.3), 0.2 M AmSO4. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87313 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→40.2 Å / Num. obs: 55338 / % possible obs: 98.2 % / Redundancy: 13.2 % / Biso Wilson estimate: 24.77 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.07987 / Rpim(I) all: 0.02283 / Rrim(I) all: 0.08319 / Net I/σ(I): 14.45 |
Reflection shell | Resolution: 1.5→1.554 Å / Redundancy: 13.3 % / Num. unique obs: 5404 / CC1/2: 0.502 / % possible all: 97.02 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2I07 Resolution: 1.5→40.19 Å / SU ML: 0.2238 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.3293
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.39 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→40.19 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 26.9114774278 Å / Origin y: 2.02166971999 Å / Origin z: -10.9014499839 Å
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Refinement TLS group | Selection details: all |