+Open data
-Basic information
Entry | Database: PDB / ID: 5l7n | ||||||||||||
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Title | Plexin A1 extracellular fragment, domains 7-10 (IPT3-IPT6) | ||||||||||||
Components | Plexin-A1 | ||||||||||||
Keywords | SIGNALING PROTEIN / IPT domain / receptor / axon guidance | ||||||||||||
Function / homology | Function and homology information olfactory nerve formation / Other semaphorin interactions / CRMPs in Sema3A signaling / RHOD GTPase cycle / Sema3A PAK dependent Axon repulsion / neuron projection guidance / dichotomous subdivision of terminal units involved in salivary gland branching / RND1 GTPase cycle / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion ...olfactory nerve formation / Other semaphorin interactions / CRMPs in Sema3A signaling / RHOD GTPase cycle / Sema3A PAK dependent Axon repulsion / neuron projection guidance / dichotomous subdivision of terminal units involved in salivary gland branching / RND1 GTPase cycle / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / semaphorin receptor complex / semaphorin receptor activity / negative regulation of cell adhesion / regulation of smooth muscle cell migration / neuron projection extension / positive regulation of axonogenesis / regulation of cell migration / regulation of cell shape / glutamatergic synapse / synapse / nucleoplasm / membrane / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 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 | 5l7n.cif.gz | 148.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l7n.ent.gz | 119.7 KB | Display | PDB format |
PDBx/mmJSON format | 5l7n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5l7n_validation.pdf.gz | 469.4 KB | Display | wwPDB validaton report |
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Full document | 5l7n_full_validation.pdf.gz | 471.1 KB | Display | |
Data in XML | 5l7n_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 5l7n_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/5l7n ftp://data.pdbj.org/pub/pdb/validation_reports/l7/5l7n | HTTPS FTP |
-Related structure data
Related structure data | 5l56C 5l59C 5l5cC 5l5gC 5l5kC 5l5lC 5l5mC 5l5nC 5l74C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 42928.707 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plxna1, Kiaa4053 / Cell line (production host): HEK293 S / Production host: Homo sapiens (human) / References: UniProt: P70206 | ||||||
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#2: Sugar | #3: Chemical | ChemComp-EDO / | #4: Chemical | ChemComp-PEG / | #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: 2.3 Å3/Da / Density % sol: 46 % |
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Crystal grow | Temperature: 293.5 K / Method: vapor diffusion, sitting drop Details: 25% (w/v) polyethylene glycol 3,350, 100mM BIS-TRIS pH 5.5 and 200mM potassium sodium tartrate |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Liquid nitrogen stream |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→62.8 Å / Num. obs: 20394 / % possible obs: 100 % / Redundancy: 8.1 % / CC1/2: 1 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 5 % / Rmerge(I) obs: 0.825 / Mean I/σ(I) obs: 1.9 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Resolution: 2.2→62.8 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.4 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→62.8 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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