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Open data
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Basic information
Entry | Database: PDB / ID: 2v9r | ||||||
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Title | First and second Ig domains from human Robo1 (Form 2) | ||||||
![]() | ROUNDABOUT HOMOLOG 1 | ||||||
![]() | RECEPTOR / PROTO-ONCOGENE / DIFFERENTIATION / PHOSPHORYLATION / DISEASE MUTATION / NEURONAL DEVELOPMENT / IMMUNOGLOBULIN DOMAIN / CHEMOTAXIS / NEUROGENESIS / GLYCOPROTEIN / TRANSMEMBRANE / ROBO1 / MEMBRANE / IG DOMAIN / ROUNDABOUT / DEVELOPMENTAL PROTEIN | ||||||
Function / homology | ![]() 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 / aortic valve morphogenesis / positive regulation of vascular endothelial growth factor receptor signaling pathway / cell migration involved in sprouting angiogenesis / axon midline choice point recognition / Activation of RAC1 / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Morlot, C. / Cusack, S. / McCarthy, A.A. | ||||||
![]() | ![]() Title: Structural Insights Into the Slit-Robo Complex. Authors: Morlot, C. / Thielens, N.M. / Ravelli, R.B. / 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.4 KB | Display | ![]() |
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PDB format | ![]() | 38.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.1 KB | Display | ![]() |
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Full document | ![]() | 439 KB | Display | |
Data in XML | ![]() | 10.2 KB | Display | |
Data in CIF | ![]() | 13.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2v9qSC ![]() 2v9sC ![]() 2v9tC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() | ||||||
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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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE |
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Crystal grow | pH: 5.6 / Details: 12% PEG 6000, 0.1M LISO4, 0.1M NA CITRATE, pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 3, 2006 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 54927 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 7 / % possible all: 94.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2V9Q Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.837 / SU B: 15.071 / SU ML: 0.218 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS IS A SECOND CRYSTAL FORM OF THE SUBMISSION ABOVE, ROBO1 IG1-2. ALTHOUGH IT DIFFRACTED TO A HIGHER RESOLUTION THE R AND RFREE ARE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS IS A SECOND CRYSTAL FORM OF THE SUBMISSION ABOVE, ROBO1 IG1-2. ALTHOUGH IT DIFFRACTED TO A HIGHER RESOLUTION THE R AND RFREE ARE LARGER THAN EXPECTED FOR THIS RESOLUTION. THIS IS PROBABLY DUE TO THE PRESENCE OF A WEAK SUPER LATTICE THAT WAS OBSERVED IN THE DIFFRACTION PATTERN.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.74 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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