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Yorodumi- PDB-6bb4: Fab/epitope complex of mouse monoclonal antibody C5.2 targeting a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bb4 | |||||||||
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Title | Fab/epitope complex of mouse monoclonal antibody C5.2 targeting a phospho-tau epitope. | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / monoclonal antibody / fab / tau / phosphorylation state -specific antibody | |||||||||
Function / homology | Function and homology information plus-end-directed organelle transport along microtubule / axonal transport / histone-dependent DNA binding / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / positive regulation of protein localization to synapse / microtubule lateral binding / tubulin complex ...plus-end-directed organelle transport along microtubule / axonal transport / histone-dependent DNA binding / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / positive regulation of protein localization to synapse / microtubule lateral binding / tubulin complex / phosphatidylinositol bisphosphate binding / main axon / regulation of long-term synaptic depression / negative regulation of kinase activity / negative regulation of tubulin deacetylation / generation of neurons / regulation of chromosome organization / positive regulation of protein localization / rRNA metabolic process / internal protein amino acid acetylation / regulation of mitochondrial fission / lipoprotein particle binding / intracellular distribution of mitochondria / axonal transport of mitochondrion / axon development / central nervous system neuron development / regulation of microtubule polymerization / microtubule polymerization / minor groove of adenine-thymine-rich DNA binding / negative regulation of mitochondrial membrane potential / dynactin binding / glial cell projection / apolipoprotein binding / protein polymerization / negative regulation of mitochondrial fission / axolemma / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / positive regulation of axon extension / supramolecular fiber organization / Activation of AMPK downstream of NMDARs / regulation of microtubule cytoskeleton organization / stress granule assembly / cytoplasmic microtubule organization / regulation of cellular response to heat / regulation of calcium-mediated signaling / axon cytoplasm / positive regulation of microtubule polymerization / cellular response to brain-derived neurotrophic factor stimulus / somatodendritic compartment / synapse assembly / phosphatidylinositol binding / nuclear periphery / cellular response to nerve growth factor stimulus / positive regulation of superoxide anion generation / protein phosphatase 2A binding / regulation of autophagy / astrocyte activation / synapse organization / microglial cell activation / response to lead ion / Hsp90 protein binding / regulation of synaptic plasticity / PKR-mediated signaling / protein homooligomerization / cytoplasmic ribonucleoprotein granule / memory / microtubule cytoskeleton organization / cellular response to reactive oxygen species / SH3 domain binding / neuron projection development / activation of cysteine-type endopeptidase activity involved in apoptotic process / microtubule cytoskeleton / protein-macromolecule adaptor activity / single-stranded DNA binding / cell-cell signaling / cellular response to heat / cell body / actin binding / growth cone / protein-folding chaperone binding / double-stranded DNA binding / microtubule binding / microtubule / amyloid fibril formation / sequence-specific DNA binding / dendritic spine / learning or memory / neuron projection / nuclear speck / membrane raft / axon / negative regulation of gene expression / dendrite / neuronal cell body / DNA damage response / protein kinase binding / enzyme binding / mitochondrion / DNA binding Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 Å | |||||||||
Authors | Chukwu, J.E. / Kong, X.-P. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Sci Rep / Year: 2018 Title: Tau Antibody Structure Reveals a Molecular Switch Defining a Pathological Conformation of the Tau Protein. Authors: Chukwu, J.E. / Pedersen, J.T. / Pedersen, L.O. / Volbracht, C. / Sigurdsson, E.M. / Kong, X.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bb4.cif.gz | 274.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bb4.ent.gz | 227.9 KB | Display | PDB format |
PDBx/mmJSON format | 6bb4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/6bb4 ftp://data.pdbj.org/pub/pdb/validation_reports/bb/6bb4 | 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 on special symmetry positions |
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-Components
#1: Antibody | Mass: 23574.035 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) #2: Antibody | Mass: 23728.580 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) #3: Protein/peptide | Mass: 2629.664 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636 #4: Chemical | #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: 2.53 Å3/Da / Density % sol: 51.43 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 25.5% polyethylene glycol 4000, 0.17 M ammonium sulfate, 15% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 20, 2015 Details: Flat bent collimating Rh coated mirror, toroidal focussing mirror |
Radiation | Monochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.099→44.25 Å / Num. obs: 84763 / % possible obs: 99.51 % / Redundancy: 4.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06924 / Rpim(I) all: 0.03851 / Rrim(I) all: 0.07945 / Net I/σ(I): 12.34 |
Reflection shell | Resolution: 2.099→2.174 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.5445 / Mean I/σ(I) obs: 2.51 / Num. unique obs: 8330 / CC1/2: 0.89 / Rpim(I) all: 0.3028 / Rrim(I) all: 0.6245 / % possible all: 99.32 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.099→44.25 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.099→44.25 Å
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