+Open data
-Basic information
Entry | Database: PDB / ID: 5zry | ||||||
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Title | Crystal Structure of EphA6/Odin Complex | ||||||
Components | Ankyrin repeat and SAM domain-containing protein 1A,Ephrin type-A receptor 6 | ||||||
Keywords | PROTEIN BINDING / SAM DOMAIN / HETERODIMER / SIGNALING PROTEIN / CELL SIGNALING / RECEPTOR / TRANSMEMBRANE / TYROSINE-PROTEIN KINASE / CELL ADHESION | ||||||
Function / homology | Function and homology information regulation of ephrin receptor signaling pathway / EPH-Ephrin signaling / EPHA-mediated growth cone collapse / substrate-dependent cell migration / EPH-ephrin mediated repulsion of cells / transmembrane-ephrin receptor activity / multicellular organism development / positive regulation of kinase activity / neuron remodeling / plasma membrane => GO:0005886 ...regulation of ephrin receptor signaling pathway / EPH-Ephrin signaling / EPHA-mediated growth cone collapse / substrate-dependent cell migration / EPH-ephrin mediated repulsion of cells / transmembrane-ephrin receptor activity / multicellular organism development / positive regulation of kinase activity / neuron remodeling / plasma membrane => GO:0005886 / ephrin receptor signaling pathway / transmembrane receptor protein tyrosine kinase activity / negative regulation of ubiquitin-dependent protein catabolic process / cell surface receptor protein tyrosine kinase signaling pathway / ephrin receptor binding / axon guidance / receptor protein-tyrosine kinase / receptor complex / neuron projection / nucleoplasm / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Wang, Y. / Shang, Y. / Li, J. / Chen, W. / Li, G. / Wan, J. / Liu, W. / Zhang, M. | ||||||
Funding support | China, 1items
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Citation | Journal: Elife / Year: 2018 Title: Specific Eph receptor-cytoplasmic effector signaling mediated by SAM-SAM domain interactions. Authors: Wang, Y. / Shang, Y. / Li, J. / Chen, W. / Li, G. / Wan, J. / Liu, W. / Zhang, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zry.cif.gz | 172.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zry.ent.gz | 136.5 KB | Display | PDB format |
PDBx/mmJSON format | 5zry.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zry_validation.pdf.gz | 490.6 KB | Display | wwPDB validaton report |
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Full document | 5zry_full_validation.pdf.gz | 495.6 KB | Display | |
Data in XML | 5zry_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 5zry_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/5zry ftp://data.pdbj.org/pub/pdb/validation_reports/zr/5zry | HTTPS FTP |
-Related structure data
Related structure data | 5zrxC 5zrzC 2lmrS 3kkaS 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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Unit cell |
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Details | The biological assembly is heterodimer of two SAM domains. However, two domains were expressed as a fused single chain protein in this structure. |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 21896.809 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Odin SAM1 - EphA6 SAM fusion protein / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Anks1a, Anks1, Kiaa0229, Odin, Epha6, Ehk-2, Ehk2 / Production host: Escherichia coli (E. coli) References: UniProt: P59672, UniProt: Q62413, receptor protein-tyrosine kinase |
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-Non-polymers , 5 types, 392 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-EPE / | #5: Chemical | ChemComp-TRS / | #6: Water | ChemComp-HOH / | |
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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: 1.86 Å3/Da / Density % sol: 33.94 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 7.5 Details: 0.1M HEPES sodium pH 7.5, 1.5M lithium sulfate monohydrate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 14, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.3→50 Å / Num. obs: 79398 / % possible obs: 97.8 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.024 / Rrim(I) all: 0.059 / Χ2: 1.647 / Net I/σ(I): 11.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KKA, 2LMR Resolution: 1.3→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.304 / SU ML: 0.042 / SU R Cruickshank DPI: 0.0574 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.053 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 204.75 Å2 / Biso mean: 23.418 Å2 / Biso min: 12.1 Å2
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Refinement step | Cycle: final / Resolution: 1.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.301→1.335 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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