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Yorodumi- PDB-4xxd: Crystal Structure of mid-region amyloid beta capture by solanezumab -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xxd | ||||||
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Title | Crystal Structure of mid-region amyloid beta capture by solanezumab | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Fab / Amyloid-beta | ||||||
Function / homology | Function and homology information IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / regulation of epidermal growth factor-activated receptor activity / CD22 mediated BCR regulation / signaling receptor activator activity / collateral sprouting in absence of injury / cytosolic mRNA polyadenylation / microglia development ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / regulation of epidermal growth factor-activated receptor activity / CD22 mediated BCR regulation / signaling receptor activator activity / collateral sprouting in absence of injury / cytosolic mRNA polyadenylation / microglia development / regulation of synapse structure or activity / complement-dependent cytotoxicity / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / smooth endoplasmic reticulum calcium ion homeostasis / axon midline choice point recognition / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / regulation of Wnt signaling pathway / mating behavior / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / ciliary rootlet / Fc-gamma receptor I complex binding / Lysosome Vesicle Biogenesis / PTB domain binding / Golgi-associated vesicle / Classical antibody-mediated complement activation / positive regulation of amyloid fibril formation / neuron remodeling / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / : / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / Initial triggering of complement / presynaptic active zone / nuclear envelope lumen / modulation of excitatory postsynaptic potential / suckling behavior / COPII-coated ER to Golgi transport vesicle / immunoglobulin complex, circulating / IgG immunoglobulin complex / dendrite development / immunoglobulin receptor binding / smooth endoplasmic reticulum / regulation of NMDA receptor activity / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / neuromuscular process controlling balance / regulation of presynapse assembly / The NLRP3 inflammasome / immunoglobulin mediated immune response / intracellular copper ion homeostasis / transition metal ion binding / regulation of multicellular organism growth / negative regulation of long-term synaptic potentiation / FCGR activation / negative regulation of neuron differentiation / ECM proteoglycans / spindle midzone / positive regulation of T cell migration / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / complement activation, classical pathway / forebrain development / regulation of peptidyl-tyrosine phosphorylation / positive regulation of chemokine production / clathrin-coated pit / Notch signaling pathway / antigen binding / positive regulation of G2/M transition of mitotic cell cycle / ionotropic glutamate receptor signaling pathway / positive regulation of protein metabolic process / neuron projection maintenance / cholesterol metabolic process / extracellular matrix organization / positive regulation of glycolytic process / positive regulation of mitotic cell cycle / response to interleukin-1 / axonogenesis / adult locomotory behavior / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / trans-Golgi network membrane / dendritic shaft / locomotory behavior / platelet alpha granule lumen / positive regulation of peptidyl-threonine phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / learning / central nervous system development / positive regulation of interleukin-1 beta production / positive regulation of long-term synaptic potentiation / Regulation of Complement cascade / astrocyte activation / endosome lumen / Cell surface interactions at the vascular wall Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å | ||||||
Authors | Hermans, S.J. / Crespi, G.A.N. / Parker, M.W. / Miles, L.A. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Sci Rep / Year: 2015 Title: Molecular basis for mid-region amyloid-beta capture by leading Alzheimer's disease immunotherapies. Authors: Crespi, G.A. / Hermans, S.J. / Parker, M.W. / Miles, L.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xxd.cif.gz | 341 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xxd.ent.gz | 280.5 KB | Display | PDB format |
PDBx/mmJSON format | 4xxd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xx/4xxd ftp://data.pdbj.org/pub/pdb/validation_reports/xx/4xxd | HTTPS FTP |
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-Related structure data
Related structure data | 4hixS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 24062.852 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pcDNA3.1+ / Cell line (production host): 292-F / Production host: Homo sapiens (human) / References: UniProt: P01834*PLUS #2: Antibody | Mass: 23714.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pcDNA3.1+ / Cell line (production host): 293-F / Production host: Homo sapiens (human) / References: UniProt: P01857*PLUS #3: Protein/peptide | Mass: 1959.207 Da / Num. of mol.: 2 / Fragment: UNP residues 683-699 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05067 #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.24 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: PEG 3350, sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.41→46.56 Å / Num. obs: 35968 / % possible obs: 97.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 43.25 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.41→2.51 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 2.3 / % possible all: 91.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4HIX Resolution: 2.41→46.56 Å / Cor.coef. Fo:Fc: 0.8628 / Cor.coef. Fo:Fc free: 0.8116 / SU R Cruickshank DPI: 0.543 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.51 / SU Rfree Blow DPI: 0.298 / SU Rfree Cruickshank DPI: 0.307
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Displacement parameters | Biso mean: 38.44 Å2
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Refine analyze | Luzzati coordinate error obs: 0.445 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.41→46.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.41→2.48 Å / Total num. of bins used: 18
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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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