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Yorodumi- PDB-5nbq: The structure of the tripartite complex between OspE, the C-termi... -
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-Basic information
Entry | Database: PDB / ID: 5nbq | |||||||||
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Title | The structure of the tripartite complex between OspE, the C-terminal domains of factor H and C3dg | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / complement / regulation / microbe / evasion | |||||||||
Function / homology | Function and homology information regulation of complement activation, alternative pathway / symbiont cell surface / oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / complement component C3b binding / regulation of complement-dependent cytotoxicity / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance ...regulation of complement activation, alternative pathway / symbiont cell surface / oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / complement component C3b binding / regulation of complement-dependent cytotoxicity / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / regulation of complement activation / complement-mediated synapse pruning / Alternative complement activation / positive regulation of lipid storage / positive regulation of phagocytosis, engulfment / positive regulation of G protein-coupled receptor signaling pathway / 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 / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation, alternative pathway / complement activation / endopeptidase inhibitor activity / neuron remodeling / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production / Purinergic signaling in leishmaniasis infection / Peptide ligand-binding receptors / complement activation, classical pathway / fatty acid metabolic process / Regulation of Complement cascade / Post-translational protein phosphorylation / response to bacterium / positive regulation of receptor-mediated endocytosis / positive regulation of angiogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / heparin binding / G alpha (i) signalling events / secretory granule lumen / blood microparticle / inflammatory response / immune 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 / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Borreliella burgdorferi (Lyme disease spirochete) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.18 Å | |||||||||
Authors | Kolodziejczyk, R. / Mikula, K.M. / Kotila, T.M. / Postis, V.L.G. / Sakari, J.T. / Meri, T. | |||||||||
Funding support | Finland, 2items
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Citation | Journal: PLoS ONE / Year: 2017 Title: Crystal structure of a tripartite complex between C3dg, C-terminal domains of factor H and OspE of Borrelia burgdorferi. Authors: Kolodziejczyk, R. / Mikula, K.M. / Kotila, T. / Postis, V.L.G. / Jokiranta, T.S. / Goldman, A. / Meri, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nbq.cif.gz | 583.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nbq.ent.gz | 500.1 KB | Display | PDB format |
PDBx/mmJSON format | 5nbq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/5nbq ftp://data.pdbj.org/pub/pdb/validation_reports/nb/5nbq | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 32824.590 Da / Num. of mol.: 3 / Mutation: A1153E, C1010A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: C3, CPAMD1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01024 #2: Protein | Mass: 14443.388 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CFH, HF, HF1, HF2 / Production host: Pichia (fungus) / References: UniProt: P08603 #3: Protein | Mass: 14385.098 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete) Gene: OspE / Production host: Escherichia coli (E. coli) / References: UniProt: Q45001 #4: Protein | | Mass: 14810.617 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete) Gene: OspE / Production host: Escherichia coli (E. coli) / References: UniProt: Q45001 #5: 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: 2.55 Å3/Da / Density % sol: 51.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG3350, 0.1 M HEPES pH 7.5, 0.2 M MgCl2 or 24% PEG3350, 0.1 M HEPES pH 7.5, 0.2 M MgCl2 or 16% PEG3350, Tris pH 8.5, 0.2 M ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 1, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.969 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.18→29.6 Å / Num. obs: 29070 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 6.419 % / Biso Wilson estimate: 78.73 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.135 / Rrim(I) all: 0.147 / Χ2: 1.038 / Net I/σ(I): 12.43 / Num. measured all: 186599 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.18→29.6 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.878 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.519
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Displacement parameters | Biso max: 287.66 Å2 / Biso mean: 91.13 Å2 / Biso min: 20.15 Å2
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Refine analyze | Luzzati coordinate error obs: 0.5 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.18→29.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.18→3.29 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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