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- PDB-5zv3: Crystal structure of human anti-tau antibody CBTAU-28.1 in comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5zv3 | ||||||
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Title | Crystal structure of human anti-tau antibody CBTAU-28.1 in complex with its tau peptide | ||||||
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![]() | IMMUNE SYSTEM / antibody / tau protein / peptide antigen | ||||||
Function / homology | ![]() 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 / 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 / lipoprotein particle binding / dynactin binding / apolipoprotein binding / glial cell projection / negative regulation of mitochondrial membrane potential / 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 / regulation of microtubule cytoskeleton organization / Activation of AMPK downstream of NMDARs / supramolecular fiber organization / regulation of cellular response to heat / stress granule assembly / cytoplasmic microtubule organization / regulation of calcium-mediated signaling / axon cytoplasm / positive regulation of microtubule polymerization / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / 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 / response to lead ion / synapse organization / microglial cell activation / Hsp90 protein binding / regulation of synaptic plasticity / PKR-mediated signaling / protein homooligomerization / memory / cytoplasmic ribonucleoprotein granule / microtubule cytoskeleton organization / cellular response to reactive oxygen species / SH3 domain binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / microtubule cytoskeleton / neuron projection development / cell-cell signaling / protein-macromolecule adaptor activity / actin binding / single-stranded DNA binding / cellular response to heat / protein-folding chaperone binding / cell body / growth cone / microtubule binding / double-stranded DNA binding / microtubule / amyloid fibril formation / sequence-specific DNA binding / dendritic spine / learning or memory / nuclear speck / neuron projection / membrane raft / axon / negative regulation of gene expression / neuronal cell body / DNA damage response / dendrite / protein kinase binding / enzyme binding / mitochondrion / DNA binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, H. / Wilson, I.A. | ||||||
![]() | ![]() Title: A common antigenic motif recognized by naturally occurring human VH5-51/VL4-1 anti-tau antibodies with distinct functionalities. Authors: Apetri, A. / Crespo, R. / Juraszek, J. / Pascual, G. / Janson, R. / Zhu, X. / Zhang, H. / Keogh, E. / Holland, T. / Wadia, J. / Verveen, H. / Siregar, B. / Mrosek, M. / Taggenbrock, R. / ...Authors: Apetri, A. / Crespo, R. / Juraszek, J. / Pascual, G. / Janson, R. / Zhu, X. / Zhang, H. / Keogh, E. / Holland, T. / Wadia, J. / Verveen, H. / Siregar, B. / Mrosek, M. / Taggenbrock, R. / Ameijde, J. / Inganas, H. / van Winsen, M. / Koldijk, M.H. / Zuijdgeest, D. / Borgers, M. / Dockx, K. / Stoop, E.J.M. / Yu, W. / Brinkman-van der Linden, E.C. / Ummenthum, K. / van Kolen, K. / Mercken, M. / Steinbacher, S. / de Marco, D. / Hoozemans, J.J. / Wilson, I.A. / Koudstaal, W. / Goudsmit, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.6 KB | Display | ![]() |
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PDB format | ![]() | 78.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448 KB | Display | ![]() |
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Full document | ![]() | 449.6 KB | Display | |
Data in XML | ![]() | 19.6 KB | Display | |
Data in CIF | ![]() | 28.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6dcvC ![]() 6dcwC ![]() 6gk7C ![]() 6gk8C ![]() 3qot S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein/peptide | Mass: 2025.963 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#2: Antibody | Mass: 24420.314 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Antibody | Mass: 24242.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.085M Tris-HCl, pH 8.5, 0.17M sodium acetate, 25.5% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 2, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→50 Å / Num. obs: 25910 / % possible obs: 97.5 % / Redundancy: 3.4 % / CC1/2: 0.985 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.08 / Rrim(I) all: 0.15 / Rsym value: 0.12 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3146 / CC1/2: 0.65 / Rpim(I) all: 0.65 / Rsym value: 0.86 / % possible all: 78.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3QOT ![]() 3qot Resolution: 2.093→41.223 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.5
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.093→41.223 Å
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Refine LS restraints |
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LS refinement shell |
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