+Open data
-Basic information
Entry | Database: PDB / ID: 2v9q | ||||||
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Title | First and second Ig domains from human Robo1 | ||||||
Components | ROUNDABOUT HOMOLOG 1 | ||||||
Keywords | RECEPTOR / PROTO-ONCOGENE / DIFFERENTIATION / PHOSPHORYLATION / DISEASE MUTATION / NEURONAL DEVELOPMENT / IMMUNOGLOBULIN DOMAIN / CHEMOTAXIS / NEUROGENESIS / GLYCOPROTEIN / TRANSMEMBRANE / ROBO1 / MEMBRANE / IG DOMAIN / ROUNDABOUT / DEVELOPMENTAL PROTEIN | ||||||
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 / axon guidance receptor activity / Netrin-1 signaling / positive regulation of vascular endothelial growth factor signaling pathway ...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 / axon guidance receptor activity / Netrin-1 signaling / positive regulation of vascular endothelial growth factor signaling pathway / Role of ABL in ROBO-SLIT signaling / Regulation of commissural axon pathfinding by SLIT and ROBO / SLIT2:ROBO1 increases RHOA activity / Roundabout signaling pathway / Inactivation of CDC42 and RAC1 / endocardial cushion formation / Signaling by ROBO receptors / pulmonary valve morphogenesis / outflow tract septum morphogenesis / positive regulation of vascular endothelial growth factor receptor signaling pathway / cell migration involved in sprouting angiogenesis / aortic valve morphogenesis / Activation of RAC1 / 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 / positive regulation of MAP kinase activity / negative regulation of cell migration / activation of cysteine-type endopeptidase activity involved in apoptotic process / Regulation of expression of SLITs and ROBOs / nervous system development / cell adhesion / neuron projection / axon / negative regulation of gene expression / 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 / MAD / Resolution: 2.5 Å | ||||||
Authors | Morlot, C. / Cusack, S. / McCarthy, A.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2007 Title: Structural Insights Into the Slit-Robo Complex. Authors: Morlot, C. / Thielens, N.M. / Ravelli, R.B.G. / Hemrika, W. / Romijn, R.A. / Gros, P. / Cusack, S. / Mccarthy, A.A. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2007 Title: Cloning, Expression, Crystallization and Preliminary X-Ray Analysis of the First Two Ig Domains from Human Roundabout 1 (Robo1). Authors: Morlot, C. / Hemrika, W. / Romijn, R.A. / Gros, P. / Cusack, S. / Mccarthy, A.A. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v9q.cif.gz | 52.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v9q.ent.gz | 40.3 KB | Display | PDB format |
PDBx/mmJSON format | 2v9q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v9/2v9q ftp://data.pdbj.org/pub/pdb/validation_reports/v9/2v9q | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 23587.717 Da / Num. of mol.: 1 / Fragment: IG1-2M, RESIDUES 61-266 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293-EBNA1 / Production host: HOMO SAPIENS (human) / References: UniProt: Q9Y6N7 | ||||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | A N160D MUTATION WAS MADE TO PREVENT POTENTIAL GLYCOSYLAT | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 18-20% PEG 3350, 0.2M K THIOCYNATE, 0.1M MES, PH=6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.009 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 19, 2006 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.009 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 32973 / % possible obs: 93.1 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.5 / % possible all: 71.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.9 / SU B: 20.896 / SU ML: 0.23 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.472 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.73 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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