+Open data
-Basic information
Entry | Database: PDB / ID: 2wfh | ||||||
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Title | The Human Slit 2 Dimerization Domain D4 | ||||||
Components | SLIT HOMOLOG 2 PROTEIN C-PRODUCT | ||||||
Keywords | SPLICING / DEVELOPMENTAL PROTEIN / NEUROGENESIS / GLYCOPROTEIN / LEUCINE-RICH REPEAT / DISULFIDE BOND / DIFFERENTIATION / EGF-LIKE DOMAIN / ID14-EH4 / ROUNDABOUT / CHEMOTAXIS / NERVE CELL / MIDLINE / HEPARAN / HEPARIN / SECRETED / GUIDANCE / D4 / XDS / LRR / SLIT / AXON / NEURON / PHASER / SULFATE | ||||||
Function / homology | Function and homology information negative regulation of leukocyte chemotaxis / corticospinal neuron axon guidance through spinal cord / negative regulation of lamellipodium assembly / induction of negative chemotaxis / negative regulation of mononuclear cell migration / negative regulation of retinal ganglion cell axon guidance / apoptotic process involved in luteolysis / negative regulation of monocyte chemotaxis / chemorepulsion involved in postnatal olfactory bulb interneuron migration / Roundabout binding ...negative regulation of leukocyte chemotaxis / corticospinal neuron axon guidance through spinal cord / negative regulation of lamellipodium assembly / induction of negative chemotaxis / negative regulation of mononuclear cell migration / negative regulation of retinal ganglion cell axon guidance / apoptotic process involved in luteolysis / negative regulation of monocyte chemotaxis / chemorepulsion involved in postnatal olfactory bulb interneuron migration / Roundabout binding / negative regulation of smooth muscle cell chemotaxis / negative regulation of cellular response to growth factor stimulus / cellular response to heparin / negative regulation of small GTPase mediated signal transduction / negative regulation of chemokine-mediated signaling pathway / response to cortisol / laminin-1 binding / negative regulation of smooth muscle cell migration / axon extension involved in axon guidance / Netrin-1 signaling / GTPase inhibitor activity / Role of ABL in ROBO-SLIT signaling / Regulation of commissural axon pathfinding by SLIT and ROBO / negative regulation of neutrophil chemotaxis / Inactivation of CDC42 and RAC1 / SLIT2:ROBO1 increases RHOA activity / Roundabout signaling pathway / negative regulation of actin filament polymerization / Signaling by ROBO receptors / pulmonary valve morphogenesis / negative regulation of vascular permeability / motor neuron axon guidance / cell migration involved in sprouting angiogenesis / Activation of RAC1 / aortic valve morphogenesis / retinal ganglion cell axon guidance / proteoglycan binding / negative regulation of endothelial cell migration / ureteric bud development / negative chemotaxis / positive regulation of axonogenesis / ventricular septum morphogenesis / branching morphogenesis of an epithelial tube / cellular response to hormone stimulus / negative regulation of cell migration / negative regulation of protein phosphorylation / axon guidance / negative regulation of cell growth / Regulation of expression of SLITs and ROBOs / heparin binding / positive regulation of apoptotic process / calcium ion binding / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Seiradake, E. / von Philipsborn, A.C. / Henry, M. / Fritz, M. / Lortat-Jacob, H. / Jamin, M. / Hemrika, W. / Bastmeyer, M. / Cusack, S. / McCarthy, A.A. | ||||||
Citation | Journal: EMBO Rep. / Year: 2009 Title: Structure and functional relevance of the Slit2 homodimerization domain. Authors: Seiradake, E. / von Philipsborn, A.C. / Henry, M. / Fritz, M. / Lortat-Jacob, H. / Jamin, M. / Hemrika, W. / Bastmeyer, M. / Cusack, S. / 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 | 2wfh.cif.gz | 90.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wfh.ent.gz | 67.9 KB | Display | PDB format |
PDBx/mmJSON format | 2wfh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/2wfh ftp://data.pdbj.org/pub/pdb/validation_reports/wf/2wfh | HTTPS FTP |
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-Related structure data
Related structure data | 2v70S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21460.699 Da / Num. of mol.: 2 / Fragment: DIMERIZATION DOMAIN, RESIDUES 726-907 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: MODIFIED PTT3 Cell line (production host): HUMAN EMBRYONIC KIDNEY CELLS (HEK 293 EBNA) Production host: HOMO SAPIENS (human) / References: UniProt: O94813 #2: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | Sequence details | CONSTRUCT CONTAINS N-TERMINAL RESIDUES GS AND C-TERMINAL RESIDUES AAAHHHHHH | |
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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: 2.25 Å3/Da / Density % sol: 45.02 % Description: THE INPUT MODEL WAS EDITED TO CONTAIN THE SAME NUMBER OF LRR REPEATS AS THE TARGET. |
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Crystal grow | pH: 8.5 / Details: 0.2 M LISO4, 0.1 M TRIS PH 8.5, 30% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→45.5 Å / Num. obs: 36353 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.8→1.9 Å / Mean I/σ(I) obs: 3.8 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V70 Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.673 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.122 / 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: 21.937 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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