+Open data
-Basic information
Entry | Database: PDB / ID: 8oq3 | ||||||||||||
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Title | Structure of methylamine treated human complement C3 | ||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / innate immune system / complement / activation / 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 phagocytosis, engulfment ...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 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 D-glucose transmembrane transport / complement-dependent cytotoxicity / complement activation, alternative pathway / complement activation / endopeptidase inhibitor activity / neuron remodeling / B cell activation / 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 / response to bacterium / Post-translational protein phosphorylation / 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 / G alpha (i) signalling events / secretory granule lumen / blood microparticle / receptor ligand activity / 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 / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Lama glama (llama) Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||||||||
Authors | Gadeberg, T.A.F. / Andersen, G.R. | ||||||||||||
Funding support | Denmark, 3items
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Citation | Journal: To Be Published Title: Structure of methylamine treated human complement C3 Authors: 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 | 8oq3.cif.gz | 668.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8oq3.ent.gz | 536.6 KB | Display | PDB format |
PDBx/mmJSON format | 8oq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8oq3_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8oq3_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8oq3_validation.xml.gz | 94.9 KB | Display | |
Data in CIF | 8oq3_validation.cif.gz | 144.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/8oq3 ftp://data.pdbj.org/pub/pdb/validation_reports/oq/8oq3 | HTTPS FTP |
-Related structure data
Related structure data | 17103MC M: map data used to model this data C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 185173.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: this is a two chain protein, see uniprot entry co3_human. Compared to this entry, the signal peptide is missing and furin cleavage has removed residues 668-671. the remaining residues are in ...Details: this is a two chain protein, see uniprot entry co3_human. Compared to this entry, the signal peptide is missing and furin cleavage has removed residues 668-671. the remaining residues are in the molecule but not modelled Source: (natural) Homo sapiens (human) / References: UniProt: P01024 #2: Antibody | Mass: 14203.742 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight |
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Source (natural) |
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Buffer solution | pH: 7 | ||||||||||||||||||||||||
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2438 nm / Nominal defocus min: 170 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 59.5 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 197438 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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