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Yorodumi- PDB-5l74: Plexin A2 extracellular segment domains 4-5 (PSI2-IPT2), resoluti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5l74 | ||||||||||||
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Title | Plexin A2 extracellular segment domains 4-5 (PSI2-IPT2), resolution 1.36 Angstrom | ||||||||||||
Components | Plexin-A2 | ||||||||||||
Keywords | SIGNALING PROTEIN / receptor / axon guidance / PSI-IPT domains | ||||||||||||
Function / homology | Function and homology information cerebellar granule cell precursor tangential migration / CRMPs in Sema3A signaling / Sema3A PAK dependent Axon repulsion / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / semaphorin-plexin signaling pathway involved in axon guidance / limb bud formation / semaphorin receptor complex / pharyngeal system development / semaphorin receptor activity / negative regulation of cell adhesion ...cerebellar granule cell precursor tangential migration / CRMPs in Sema3A signaling / Sema3A PAK dependent Axon repulsion / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / semaphorin-plexin signaling pathway involved in axon guidance / limb bud formation / semaphorin receptor complex / pharyngeal system development / semaphorin receptor activity / negative regulation of cell adhesion / neural tube development / centrosome localization / positive regulation of axonogenesis / semaphorin-plexin signaling pathway / somitogenesis / regulation of cell migration / regulation of cell shape / collagen-containing extracellular matrix / cell surface receptor signaling pathway / identical protein binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å | ||||||||||||
Authors | Kong, Y. / Janssen, B.J.C. / Malinauskas, T. / Vangoor, V.R. / Coles, C.H. / Kaufmann, R. / Ni, T. / Gilbert, R.J.C. / Padilla-Parra, S. / Pasterkamp, R.J. / Jones, E.Y. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Neuron / Year: 2016 Title: Structural Basis for Plexin Activation and Regulation. Authors: Kong, Y. / Janssen, B.J. / Malinauskas, T. / Vangoor, V.R. / Coles, C.H. / Kaufmann, R. / Ni, T. / Gilbert, R.J. / Padilla-Parra, S. / Pasterkamp, R.J. / Jones, E.Y. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l74.cif.gz | 77.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l74.ent.gz | 59.4 KB | Display | PDB format |
PDBx/mmJSON format | 5l74.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/5l74 ftp://data.pdbj.org/pub/pdb/validation_reports/l7/5l74 | HTTPS FTP |
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-Related structure data
Related structure data | 5l56C 5l59C 5l5cC 5l5gC 5l5kC 5l5lC 5l5mC 5l5nC 5l7nC C: citing same article (ref.) |
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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: 16905.119 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plxna2, Kiaa0463 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P70207 | ||||||
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#2: Sugar | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: 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: 2.27 Å3/Da / Density % sol: 45.73 % |
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Crystal grow | Temperature: 293.5 K / Method: vapor diffusion, sitting drop Details: 25% (w/v) polyethylene glycol 3,350 and 100 mM BIS-TRIS pH 5.5 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.0163 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Dec 8, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0163 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→52.1 Å / Num. obs: 27859 / % possible obs: 85.6 % / Redundancy: 3.7 % / Net I/σ(I): 17 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→52.092 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.79
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.36→52.092 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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