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Yorodumi- PDB-5l5l: Plexin A4 full extracellular region, domains 1 to 8 modeled, data... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5l5l | ||||||
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Title | Plexin A4 full extracellular region, domains 1 to 8 modeled, data to 8 angstrom, spacegroup P2(1) | ||||||
Components | Plexin-A4 | ||||||
Keywords | SIGNALING PROTEIN / receptor / signaling / axon guidance | ||||||
Function / homology | Function and homology information glossopharyngeal nerve morphogenesis / chemorepulsion of branchiomotor axon / regulation of negative chemotaxis / vagus nerve morphogenesis / cranial nerve morphogenesis / trigeminal nerve morphogenesis / anterior commissure morphogenesis / regulation of axon extension involved in axon guidance / postganglionic parasympathetic fiber development / facial nerve morphogenesis ...glossopharyngeal nerve morphogenesis / chemorepulsion of branchiomotor axon / regulation of negative chemotaxis / vagus nerve morphogenesis / cranial nerve morphogenesis / trigeminal nerve morphogenesis / anterior commissure morphogenesis / regulation of axon extension involved in axon guidance / postganglionic parasympathetic fiber development / facial nerve morphogenesis / sympathetic neuron axon guidance / CRMPs in Sema3A signaling / Sema3A PAK dependent Axon repulsion / trigeminal nerve structural organization / facial nerve structural organization / branchiomotor neuron axon guidance / cerebellar climbing fiber to Purkinje cell synapse / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / maintenance of synapse structure / semaphorin receptor complex / sympathetic nervous system development / semaphorin receptor activity / negative regulation of cell adhesion / embryonic heart tube development / motor neuron axon guidance / positive regulation of axonogenesis / semaphorin-plexin signaling pathway / neuron projection morphogenesis / regulation of cell migration / axon guidance / nervous system development / regulation of cell shape / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 8.001 Å | ||||||
Authors | Janssen, B.J.C. / Kong, Y. / 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. | ||||||
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 | 5l5l.cif.gz | 351.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l5l.ent.gz | 264.6 KB | Display | PDB format |
PDBx/mmJSON format | 5l5l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5l5l_validation.pdf.gz | 443.9 KB | Display | wwPDB validaton report |
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Full document | 5l5l_full_validation.pdf.gz | 641.4 KB | Display | |
Data in XML | 5l5l_validation.xml.gz | 70.1 KB | Display | |
Data in CIF | 5l5l_validation.cif.gz | 97.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l5/5l5l ftp://data.pdbj.org/pub/pdb/validation_reports/l5/5l5l | HTTPS FTP |
-Related structure data
Related structure data | 5l56SC 5l59C 5l5cC 5l5gC 5l5kC 5l5mC 5l5nC 5l74C 5l7nC S: Starting model for refinement 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 134813.844 Da / Num. of mol.: 2 / Fragment: UNP residues 36-1229 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plxna4, Kiaa1550 / Cell line (production host): Hek293 / Production host: Homo sapiens (human) / References: UniProt: Q80UG2 |
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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 % sol: 84 % |
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Crystal grow | Temperature: 293.5 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.5 M sodium succinate, 100 mM bis-TRIS propane, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 13, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 8→48 Å / Num. obs: 10061 / % possible obs: 99.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.158 / Net I/σ(I): 9 |
Reflection shell | Highest resolution: 8 Å / Rmerge(I) obs: 0.764 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5L56 Resolution: 8.001→47.741 Å / SU ML: 1.53 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 39.92 Details: THE AUTHORS STATE THAT DUE TO THE LOW RESOLUTION OF THE DIFFRACTION DATA THE STRUCTURE WAS ONLY SUBJECTED TO RIGID BODY REFINEMENT WITH EACH DOMAIN AS RIGID BODY. THE STRUCTURE IS BASED ON A ...Details: THE AUTHORS STATE THAT DUE TO THE LOW RESOLUTION OF THE DIFFRACTION DATA THE STRUCTURE WAS ONLY SUBJECTED TO RIGID BODY REFINEMENT WITH EACH DOMAIN AS RIGID BODY. THE STRUCTURE IS BASED ON A HOMOLOGY MODEL GENERATED WITH PDB ENTRY 5L56 AS TEMPLATE (53% SEQUENCE IDENTITY). THE AUTHORS HAVE NOT FURTHER REFINED THE RESULTING COORDINATES NOR CORRECTED RESULTING CLASHES BETWEEN ATOMS AND DEVIATING PEPTIDE LINKAGES BETWEEN DOMAINS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 8.001→47.741 Å
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Refine LS restraints |
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LS refinement shell |
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