+Open data
-Basic information
Entry | Database: PDB / ID: 5ywz | ||||||
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Title | AID-SUN tandem of SUN1 | ||||||
Components | SUN domain-containing protein 1 | ||||||
Keywords | NUCLEAR PROTEIN / LINC complex / SUN proteins / SUN1 / autoinhibition | ||||||
Function / homology | Function and homology information : / outer acrosomal membrane / nucleokinesis involved in cell motility in cerebral cortex radial glia guided migration / nuclear matrix anchoring at nuclear membrane / cytoskeleton-nuclear membrane anchor activity / meiotic attachment of telomere to nuclear envelope / meiotic nuclear membrane microtubule tethering complex / acrosomal membrane / nuclear envelope organization / homologous chromosome pairing at meiosis ...: / outer acrosomal membrane / nucleokinesis involved in cell motility in cerebral cortex radial glia guided migration / nuclear matrix anchoring at nuclear membrane / cytoskeleton-nuclear membrane anchor activity / meiotic attachment of telomere to nuclear envelope / meiotic nuclear membrane microtubule tethering complex / acrosomal membrane / nuclear envelope organization / homologous chromosome pairing at meiosis / lamin binding / centrosome localization / response to mechanical stimulus / protein-membrane adaptor activity / ossification / nuclear envelope / spermatogenesis / nuclear membrane / membrane => GO:0016020 / intracellular membrane-bounded organelle / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Xu, Y. / Li, W. / Feng, W. | ||||||
Funding support | China, 1items
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Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2018 Title: Structural conservation of the autoinhibitory domain in SUN proteins Authors: Xu, Y. / Li, W. / Ke, H. / Feng, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ywz.cif.gz | 65.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ywz.ent.gz | 45.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ywz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/5ywz ftp://data.pdbj.org/pub/pdb/validation_reports/yw/5ywz | HTTPS FTP |
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-Related structure data
Related structure data | 5ed8S S: Starting model for refinement |
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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
#1: Protein | Mass: 27084.549 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sun1, Unc84a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9D666 |
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#2: 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: 2.82 Å3/Da / Density % sol: 56.32 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1M MES pH 6.3, 0.6M MgSO4 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 22, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→50 Å / Num. obs: 18348 / % possible obs: 99.9 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.033 / Rrim(I) all: 0.104 / Χ2: 0.973 / Net I/σ(I): 7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ED8 Resolution: 2.2→34.442 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.91
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.9 Å2 / Biso mean: 27.6922 Å2 / Biso min: 11.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→34.442 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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