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Yorodumi- PDB-6a78: Crystal structure of the fifth immunoglobulin domain (Ig5) of hum... -
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-Basic information
Entry | Database: PDB / ID: 6a78 | ||||||
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Title | Crystal structure of the fifth immunoglobulin domain (Ig5) of human Robo1 in complex with the scFv fragment of murine monoclonal antibody B5209B | ||||||
Components |
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Keywords | IMMUNE SYSTEM / hepatocellular carcinoma antigen / angiogenesis / antibody drug / single chain Fv fragment | ||||||
Function / homology | Function and homology information chemorepulsion involved in postnatal olfactory bulb interneuron migration / negative regulation of negative chemotaxis / Regulation of cortical dendrite branching / negative regulation of mammary gland epithelial cell proliferation / LRR domain binding / negative regulation of chemokine-mediated signaling pathway / heart induction / positive regulation of vascular endothelial growth factor signaling pathway / axon guidance receptor activity / Netrin-1 signaling ...chemorepulsion involved in postnatal olfactory bulb interneuron migration / negative regulation of negative chemotaxis / Regulation of cortical dendrite branching / negative regulation of mammary gland epithelial cell proliferation / LRR domain binding / negative regulation of chemokine-mediated signaling pathway / heart induction / positive regulation of vascular endothelial growth factor signaling pathway / axon guidance receptor activity / Netrin-1 signaling / Role of ABL in ROBO-SLIT signaling / Regulation of commissural axon pathfinding by SLIT and ROBO / Inactivation of CDC42 and RAC1 / SLIT2:ROBO1 increases RHOA activity / Roundabout signaling pathway / endocardial cushion formation / Signaling by ROBO receptors / pulmonary valve morphogenesis / outflow tract septum morphogenesis / cell migration involved in sprouting angiogenesis / Activation of RAC1 / aortic valve morphogenesis / positive regulation of vascular endothelial growth factor receptor signaling pathway / axon midline choice point recognition / aorta development / positive regulation of Rho protein signal transduction / positive regulation of axonogenesis / ventricular septum morphogenesis / positive regulation of Notch signaling pathway / homophilic cell adhesion via plasma membrane adhesion molecules / endoplasmic reticulum-Golgi intermediate compartment membrane / negative regulation of cell migration / synapse organization / positive regulation of MAP kinase activity / Regulation of expression of SLITs and ROBOs / activation of cysteine-type endopeptidase activity involved in apoptotic process / nervous system development / cell adhesion / neuron projection / axon / negative regulation of gene expression / neuronal cell body / positive regulation of gene expression / cell surface / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Mizohata, E. / Nakayama, T. / Kado, Y. / Inoue, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Structure / Year: 2019 Title: Affinity Improvement of a Cancer-Targeted Antibody through Alanine-Induced Adjustment of Antigen-Antibody Interface. Authors: Yamashita, T. / Mizohata, E. / Nagatoishi, S. / Watanabe, T. / Nakakido, M. / Iwanari, H. / Mochizuki, Y. / Nakayama, T. / Kado, Y. / Yokota, Y. / Matsumura, H. / Kawamura, T. / Kodama, T. / ...Authors: Yamashita, T. / Mizohata, E. / Nagatoishi, S. / Watanabe, T. / Nakakido, M. / Iwanari, H. / Mochizuki, Y. / Nakayama, T. / Kado, Y. / Yokota, Y. / Matsumura, H. / Kawamura, T. / Kodama, T. / Hamakubo, T. / Inoue, T. / Fujitani, H. / Tsumoto, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a78.cif.gz | 139.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a78.ent.gz | 113.1 KB | Display | PDB format |
PDBx/mmJSON format | 6a78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/6a78 ftp://data.pdbj.org/pub/pdb/validation_reports/a7/6a78 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 9776.106 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ROBO1, DUTT1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6N7 #2: Antibody | Mass: 11999.374 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) #3: Antibody | Mass: 14374.789 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) #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: 2.42 Å3/Da / Density % sol: 49.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 85mM Tris-HCl (pH 8.5), 27.5% (w/v) PEG 4000, 170mM lithium sulfate monohydrate, 670mM sodium thiocyanate, 15% (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Dec 14, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 39986 / % possible obs: 95.1 % / Redundancy: 3.8 % / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.1→2.18 Å |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.913 / SU B: 7.612 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.23 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.513 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→50 Å
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Refine LS restraints |
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