+Open data
-Basic information
Entry | Database: PDB / ID: 8j1i | ||||||
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Title | Crystal Structure of EphA8/SASH1 Complex | ||||||
Components |
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Keywords | SIGNALING PROTEIN / Complex / SAM-SAM / EphA8 receptor / SASH1 | ||||||
Function / homology | Function and homology information regulation of protein K63-linked ubiquitination / regulation of protein autoubiquitination / EPH-Ephrin signaling / EPHA-mediated growth cone collapse / substrate-dependent cell migration / EPH-ephrin mediated repulsion of cells / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / regulation of epithelial cell migration / ephrin receptor activity ...regulation of protein K63-linked ubiquitination / regulation of protein autoubiquitination / EPH-Ephrin signaling / EPHA-mediated growth cone collapse / substrate-dependent cell migration / EPH-ephrin mediated repulsion of cells / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / regulation of epithelial cell migration / ephrin receptor activity / cellular response to follicle-stimulating hormone stimulus / positive regulation of lipopolysaccharide-mediated signaling pathway / mitogen-activated protein kinase kinase kinase binding / positive regulation of p38MAPK cascade / neuron remodeling / growth factor binding / regulation of cell adhesion mediated by integrin / ephrin receptor signaling pathway / G-protein alpha-subunit binding / regulation of cell adhesion / positive regulation of endothelial cell migration / axon guidance / receptor protein-tyrosine kinase / protein polyubiquitination / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of angiogenesis / neuron projection development / early endosome membrane / protein autophosphorylation / positive regulation of MAPK cascade / molecular adaptor activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / neuron projection / dendrite / protein kinase binding / protein-containing complex / nucleoplasm / ATP binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Liu, W. / Li, J. / Ding, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2023 Title: SASH1: A Novel Eph Receptor Partner and Insights into SAM-SAM Interactions. Authors: Ding, Y. / Chen, Q. / Shan, H. / Liu, J. / Lv, C. / Wang, Y. / Yuan, L. / Chen, Y. / Wang, Z. / Yin, Y. / Xiao, K. / Li, J. / Liu, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8j1i.cif.gz | 119.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8j1i.ent.gz | 92.1 KB | Display | PDB format |
PDBx/mmJSON format | 8j1i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8j1i_validation.pdf.gz | 437.3 KB | Display | wwPDB validaton report |
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Full document | 8j1i_full_validation.pdf.gz | 438.7 KB | Display | |
Data in XML | 8j1i_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 8j1i_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/8j1i ftp://data.pdbj.org/pub/pdb/validation_reports/j1/8j1i | HTTPS FTP |
-Related structure data
Related structure data | 6fxfS S: Starting model for refinement |
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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: 7489.671 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Epha8, Eek / Production host: Escherichia coli (E. coli) References: UniProt: O09127, receptor protein-tyrosine kinase |
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#2: Protein | Mass: 8497.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sash1 / Production host: Escherichia coli (E. coli) / References: UniProt: P59808 |
#3: 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: 3.12 Å3/Da / Density % sol: 60.55 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: PEG 1500,10% isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 25, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→50 Å / Num. obs: 25509 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.014 / Rrim(I) all: 0.049 / Χ2: 0.607 / Net I/σ(I): 5.9 / Num. measured all: 332592 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FXF Resolution: 1.6→32.01 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.633 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.117 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→32.01 Å
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Refine LS restraints |
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