+Open data
-Basic information
Entry | Database: PDB / ID: 7y4p | ||||||||||||
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Title | Human Plexin A1, extracellular domains 1-4 | ||||||||||||
Components | Plexin-A1 | ||||||||||||
Keywords | SIGNALING PROTEIN / Ligand binding domain of receptor | ||||||||||||
Function / homology | Function and homology information olfactory nerve formation / semaphorin-plexin signaling pathway involved in axon guidance / dichotomous subdivision of terminal units involved in salivary gland branching / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / Other semaphorin interactions / semaphorin receptor complex / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / semaphorin receptor activity / CRMPs in Sema3A signaling / negative regulation of cell adhesion ...olfactory nerve formation / semaphorin-plexin signaling pathway involved in axon guidance / dichotomous subdivision of terminal units involved in salivary gland branching / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / Other semaphorin interactions / semaphorin receptor complex / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / semaphorin receptor activity / CRMPs in Sema3A signaling / negative regulation of cell adhesion / RHOD GTPase cycle / regulation of smooth muscle cell migration / RND1 GTPase cycle / neuron projection extension / positive regulation of axonogenesis / regulation of GTPase activity / Sema3A PAK dependent Axon repulsion / regulation of cell migration / regulation of cell shape / extracellular exosome / nucleoplasm / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||||||||
Authors | Tanaka, T. / Neyazaki, M. / Nogi, T. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Protein Sci. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y4p.cif.gz | 148.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y4p.ent.gz | 113.5 KB | Display | PDB format |
PDBx/mmJSON format | 7y4p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7y4p_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7y4p_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7y4p_validation.xml.gz | 25.1 KB | Display | |
Data in CIF | 7y4p_validation.cif.gz | 33.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/7y4p ftp://data.pdbj.org/pub/pdb/validation_reports/y4/7y4p | HTTPS FTP |
-Related structure data
Related structure data | 7y4oC 7y4qC 3oktS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 77022.047 Da / Num. of mol.: 1 / Fragment: ectodomain fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLXNA1, NOV, PLXN1 / Cell line (production host): HEK293S GnT1- / Production host: Homo sapiens (human) / References: UniProt: Q9UIW2 | ||||
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#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 8.41 Å3/Da / Density % sol: 85.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.7 / Details: 1.2 M sodium potassium phosphate buffer (pH 7.7) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 18, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→49.28 Å / Num. obs: 66184 / % possible obs: 99.4 % / Redundancy: 8.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 3.5→3.67 Å / Mean I/σ(I) obs: 3 / Num. unique obs: 4366 / CC1/2: 0.94 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3OKT Resolution: 3.5→49.28 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 26.94 / 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: 3.5→49.28 Å
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Refine LS restraints |
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LS refinement shell |
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