+Open data
-Basic information
Entry | Database: PDB / ID: 6ehg | |||||||||
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Title | complement component C3b in complex with a nanobody | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Protein Complex / Inhibitor / Complement / Complement System / single domain antibody / nanobody | |||||||||
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 | Lama glama (llama) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | |||||||||
Authors | Jensen, R.K. / Andersen, K.R. / Gadeberg, T.A.F. / Laursen, N.S. / Andersen, G.R. | |||||||||
Citation | Journal: J. Biol. Chem. / Year: 2018 Title: A potent complement factor C3-specific nanobody inhibiting multiple functions in the alternative pathway of human and murine complement. Authors: Jensen, R.K. / Pihl, R. / Gadeberg, T.A.F. / Jensen, J.K. / Andersen, K.R. / Thiel, S. / Laursen, N.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 | 6ehg.cif.gz | 688.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ehg.ent.gz | 565.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ehg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eh/6ehg ftp://data.pdbj.org/pub/pdb/validation_reports/eh/6ehg | HTTPS FTP |
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-Related structure data
Related structure data | 5fo7S 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: Protein | Mass: 71265.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024 |
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#2: Protein | Mass: 104117.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024 |
#3: Antibody | Mass: 14345.896 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) |
#4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-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 |
#5: Sugar | ChemComp-NAG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.24 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 12 mM Sodium Citrate pH 8, 28 mM Sodium Citrate pH 6.0, 12.25 % (w/v) PEG 2000 MME, 70 mM Imidazole pH 7, 60 mM Ammonium acetate, 70 mM Tris pH 8.5, 13.5 % (v/v) and (+/-)-2-Methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.98021 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 29, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98021 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→62.88 Å / Num. obs: 70861 / % possible obs: 99.84 % / Redundancy: 40.4 % / Net I/σ(I): 17.42 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5fo7 Resolution: 2.65→62.88 Å / Cross valid method: FREE R-VALUE /
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Refinement step | Cycle: LAST / Resolution: 2.65→62.88 Å
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