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Open data
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Basic information
Entry | Database: PDB / ID: 7y4q | ||||||||||||
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Title | Semaphorin 6D in complex with Plexin A1 | ||||||||||||
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![]() | SIGNALING PROTEIN / signaling complex | ||||||||||||
Function / homology | ![]() Other semaphorin interactions / olfactory nerve formation / dichotomous subdivision of terminal units involved in salivary gland branching / semaphorin receptor binding / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / Other semaphorin interactions / negative regulation of smooth muscle cell migration / negative regulation of axon extension involved in axon guidance / ventricular system development / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion ...Other semaphorin interactions / olfactory nerve formation / dichotomous subdivision of terminal units involved in salivary gland branching / semaphorin receptor binding / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / Other semaphorin interactions / negative regulation of smooth muscle cell migration / negative regulation of axon extension involved in axon guidance / ventricular system development / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / semaphorin-plexin signaling pathway involved in axon guidance / chemorepellent activity / semaphorin receptor activity / CRMPs in Sema3A signaling / negative regulation of cell adhesion / RHOD GTPase cycle / regulation of smooth muscle cell migration / semaphorin receptor complex / RND1 GTPase cycle / neural crest cell migration / smooth muscle cell migration / neuron projection extension / negative chemotaxis / positive regulation of axonogenesis / regulation of GTPase activity / positive regulation of smooth muscle cell migration / semaphorin-plexin signaling pathway / Sema3A PAK dependent Axon repulsion / regulation of cell migration / axon guidance / regulation of cell shape / positive regulation of cell migration / Golgi apparatus / extracellular space / extracellular exosome / nucleoplasm / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Tanaka, T. / Neyazaki, M. / Nogi, T. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Hybrid in vitro/in silico analysis of low-affinity protein-protein interactions that regulate signal transduction by Sema6D. Authors: Tanaka, T. / Ekimoto, T. / Nagatomo, M. / Neyazaki, M. / Shimoji, E. / Yamane, T. / Kanagawa, S. / Oi, R. / Mihara, E. / Takagi, J. / Akashi, S. / Ikeguchi, M. / Nogi, T. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 592.9 KB | Display | ![]() |
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PDB format | ![]() | 390.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 84.7 KB | Display | |
Data in CIF | ![]() | 113.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7y4oC ![]() 7y4pC ![]() 7cyt ![]() 7d07 S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 77079.102 Da / Num. of mol.: 2 / Fragment: ectodomain fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 62522.633 Da / Num. of mol.: 2 / Fragment: ectodomain fragment / Mutation: S332G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 9.82 Å3/Da / Density % sol: 87.48 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 150 mM NaCl and 10 mM Tris-Cl (pH 7.4) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 4.7→49.43 Å / Num. obs: 110174 / % possible obs: 99.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 155.92 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 4.7→4.84 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.938 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4580 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7D07, 7CYT Resolution: 4.7→49.43 Å / SU ML: 0.6709 / Cross valid method: FREE R-VALUE / σ(F): 0.05 / Phase error: 27.178 / Stereochemistry target values: GeoStd + Monomer Library
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 200.63 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.7→49.43 Å
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Refine LS restraints |
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LS refinement shell |
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