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Yorodumi- PDB-5l56: Plexin A1 full extracellular region, domains 1 to 10, to 4 angstrom -
+Open data
-Basic information
Entry | Database: PDB / ID: 5l56 | |||||||||||||||
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Title | Plexin A1 full extracellular region, domains 1 to 10, to 4 angstrom | |||||||||||||||
Components | Plexin-A1 | |||||||||||||||
Keywords | SIGNALING PROTEIN / receptor / signaling / 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-plexin signaling pathway involved in axon guidance / semaphorin receptor activity / negative regulation of cell adhesion / regulation of smooth muscle cell migration / semaphorin receptor complex / neuron projection extension / positive regulation of axonogenesis / regulation of cell migration / regulation of cell shape / nucleoplasm / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||||||||
Biological species | Mus musculus (house mouse) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 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. | |||||||||||||||
Funding support | United Kingdom, 4items
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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 | 5l56.cif.gz | 263.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l56.ent.gz | 208.4 KB | Display | PDB format |
PDBx/mmJSON format | 5l56.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5l56_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 5l56_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 5l56_validation.xml.gz | 45.5 KB | Display | |
Data in CIF | 5l56_validation.cif.gz | 61.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l5/5l56 ftp://data.pdbj.org/pub/pdb/validation_reports/l5/5l56 | HTTPS FTP |
-Related structure data
Related structure data | 5l59C 5l5cC 5l5gC 5l5kC 5l5lC 5l5mC 5l5nC 5l74C 5l7nC 3oktS 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 134024.828 Da / Num. of mol.: 1 / Fragment: UNP residues 37-1236 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plxna1, Kiaa4053 / Cell line (production host): Hek293 / Production host: Homo sapiens (human) / References: UniProt: P70206 |
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-Sugars , 6 types, 10 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-NAG / | |
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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: 6.27 Å3/Da / Density % sol: 76 % |
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Crystal grow | Temperature: 293.5 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 6% (w/v) PEG 4k, 5 mM tricine or 5 mM TRIS |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 4→87 Å / Num. obs: 28954 / % possible obs: 99.1 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.241 / Net I/σ(I): 5.2 | |||||||||||||||
Reflection shell | Highest resolution: 4 Å / Rmerge(I) obs: 1.04 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3OKT Resolution: 4→87.51 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.853 / SU B: 46.776 / SU ML: 0.629 / Cross valid method: THROUGHOUT / ESU R Free: 0.748
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 133.7 Å2
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Refinement step | Cycle: LAST / Resolution: 4→87.51 Å
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