+Open data
-Basic information
Entry | Database: PDB / ID: 5o5i | ||||||
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Title | Robo1 Ig5 | ||||||
Components | Roundabout homolog 1 | ||||||
Keywords | SIGNALING PROTEIN / Neuronal receptor | ||||||
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 axonogenesis / positive regulation of Rho protein signal transduction / 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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å | ||||||
Authors | Aleksandrova, N. / Gutsche, I. / Kandiah, E. / Avilov, S.V. / Petoukhov, M.V. / Seiradake, E. / McCarthy, A.A. | ||||||
Citation | Journal: Structure / Year: 2018 Title: Robo1 Forms a Compact Dimer-of-Dimers Assembly. Authors: Aleksandrova, N. / Gutsche, I. / Kandiah, E. / Avilov, S.V. / Petoukhov, M.V. / Seiradake, E. / McCarthy, A.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o5i.cif.gz | 50.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o5i.ent.gz | 35.4 KB | Display | PDB format |
PDBx/mmJSON format | 5o5i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/5o5i ftp://data.pdbj.org/pub/pdb/validation_reports/o5/5o5i | HTTPS FTP |
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-Related structure data
Related structure data | 5o5gC 5opeC 2v9qS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/505 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9813.104 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ROBO1, DUTT1 / Plasmid: pTT3 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q9Y6N7 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 25% PEG 3350, 100 mM Sodium acetate, |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 9, 2011 / Details: Toroidal mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 2082 / % possible obs: 98.3 % / Redundancy: 3 % / Biso Wilson estimate: 74.92 Å2 / CC1/2: 0.98 / Rpim(I) all: 0.148 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 3→3.2 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1026 / CC1/2: 0.64 / Rpim(I) all: 0.798 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2v9q Resolution: 3.01→40.41 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.859 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.427
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Displacement parameters | Biso mean: 68.15 Å2
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Refine analyze | Luzzati coordinate error obs: 0.41 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.01→40.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.01→3.37 Å / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Origin x: 27.1298 Å / Origin y: -28.4573 Å / Origin z: 6.1192 Å
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Refinement TLS group | Selection details: { A|* } |