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Yorodumi- PDB-7noz: Structure of the nanobody stablized properdin bound alternative p... -
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-Basic information
Entry | Database: PDB / ID: 7noz | ||||||
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Title | Structure of the nanobody stablized properdin bound alternative pathway proconvertase C3b:FB:FP | ||||||
Components |
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Keywords | IMMUNE SYSTEM / protease / complement / cascade / proconvertase | ||||||
Function / homology | Function and homology information cytoplasmic side of Golgi membrane / alternative-complement-pathway C3/C5 convertase / positive regulation of opsonization / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / complement binding ...cytoplasmic side of Golgi membrane / alternative-complement-pathway C3/C5 convertase / positive regulation of opsonization / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / complement binding / 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 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 / 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 / specific granule lumen / 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 / positive regulation of immune response / azurophil granule lumen / tertiary granule lumen / G alpha (i) signalling events / secretory granule lumen / blood microparticle / defense response to bacterium / inflammatory response / immune response / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Lama glama (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å | ||||||
Authors | Lorenzen, J. / Pedersen, D.V. / Andersen, G.R. | ||||||
Funding support | Denmark, 1items
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Citation | Journal: Protein Sci. / Year: 2022 Title: Structure determination of an unstable macromolecular complex enabled by nanobody-peptide bridging. Authors: Lorentzen, J. / Pedersen, D.V. / Gadeberg, T.A.F. / 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 | 7noz.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7noz.ent.gz | 956.1 KB | Display | PDB format |
PDBx/mmJSON format | 7noz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/7noz ftp://data.pdbj.org/pub/pdb/validation_reports/no/7noz | HTTPS FTP |
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-Related structure data
Related structure data | 2xwbS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Complement C3 ... , 2 types, 2 molecules AB
#1: Protein | Mass: 71393.320 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: 103759.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024 |
-Protein , 3 types, 3 molecules CDF
#3: Protein | Mass: 17744.971 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CFP, PFC / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P27918 |
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#4: Protein | Mass: 22958.279 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CFP, PFC / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P27918 |
#5: Protein | Mass: 82084.609 Da / Num. of mol.: 1 / Mutation: D279G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CFB, BF, BFD / Cell line (production host): HEK293 / Production host: Homo sapiens (human) References: UniProt: P00751, alternative-complement-pathway C3/C5 convertase |
-Antibody , 1 types, 1 molecules R
#6: Antibody | Mass: 13557.077 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) |
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-Sugars , 5 types, 15 molecules
#7: Polysaccharide | Source method: isolated from a genetically manipulated source #8: Polysaccharide | Source method: isolated from a genetically manipulated source #9: Polysaccharide | Source method: isolated from a genetically manipulated source #10: Sugar | ChemComp-MAN / #11: Sugar | ChemComp-NAG / | |
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-Non-polymers , 2 types, 3 molecules
#12: Chemical | ChemComp-MG / |
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#13: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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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: 4.16 Å3/Da / Density % sol: 70.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.05 M Na-acetate pH 5.3, 0.1 M Mg-formate,7% PEG5000 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 1.033 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 23, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 3.9→48.59 Å / Num. obs: 47647 / % possible obs: 99.8 % / Redundancy: 39.7 % / Biso Wilson estimate: 196.03 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1949 / Net I/σ(I): 10.84 |
Reflection shell | Resolution: 3.9→4.039 Å / Redundancy: 43.8 % / Mean I/σ(I) obs: 0.84 / Num. unique obs: 4688 / CC1/2: 0.392 / % possible all: 99.91 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XWB Resolution: 3.9→48.59 Å / SU ML: 0.6713 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 34.0027 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 288.94 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.9→48.59 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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