+Open data
-Basic information
Entry | Database: PDB / ID: 4dxr | ||||||
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Title | Human SUN2-KASH1 complex | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / beta-sandwich / LINC complex | ||||||
Function / homology | Function and homology information negative regulation of mini excitatory postsynaptic potential / regulation of nucleus organization / nuclear migration along microfilament / nucleokinesis involved in cell motility in cerebral cortex radial glia guided migration / nuclear matrix anchoring at nuclear membrane / cytoskeleton-nuclear membrane anchor activity / meiotic nuclear membrane microtubule tethering complex / muscle cell differentiation / negative regulation of mesenchymal cell apoptotic process / lamin binding ...negative regulation of mini excitatory postsynaptic potential / regulation of nucleus organization / nuclear migration along microfilament / nucleokinesis involved in cell motility in cerebral cortex radial glia guided migration / nuclear matrix anchoring at nuclear membrane / cytoskeleton-nuclear membrane anchor activity / meiotic nuclear membrane microtubule tethering complex / muscle cell differentiation / negative regulation of mesenchymal cell apoptotic process / lamin binding / cardiac muscle cell differentiation / nuclear outer membrane / regulation of postsynaptic neurotransmitter receptor internalization / nuclear migration / nuclear inner membrane / nucleus organization / centrosome localization / positive regulation of mesenchymal cell proliferation / regulation of dendrite morphogenesis / dendritic spine head / Golgi organization / response to light stimulus / protein-membrane adaptor activity / Meiotic synapsis / sarcomere / mitotic spindle organization / meiotic cell cycle / condensed nuclear chromosome / P-body / positive regulation of receptor-mediated endocytosis / actin filament binding / nuclear envelope / actin binding / midbody / microtubule binding / postsynaptic membrane / spermatogenesis / nuclear membrane / chromosome, telomeric region / cytoskeleton / endosome membrane / positive regulation of cell migration / signaling receptor binding / nucleolus / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / protein homodimerization activity / RNA binding / nucleoplasm / membrane / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å | ||||||
Authors | Sosa, B. / Schwartz, T.U. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2012 Title: LINC Complexes Form by Binding of Three KASH Peptides to Domain Interfaces of Trimeric SUN Proteins. Authors: Sosa, B.A. / Rothballer, A. / Kutay, U. / Schwartz, T.U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dxr.cif.gz | 64.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dxr.ent.gz | 44.9 KB | Display | PDB format |
PDBx/mmJSON format | 4dxr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/4dxr ftp://data.pdbj.org/pub/pdb/validation_reports/dx/4dxr | HTTPS FTP |
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-Related structure data
Related structure data | 4dxsC 4dxtSC C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 22395.053 Da / Num. of mol.: 1 / Fragment: SUN domain (UNP residues 522-717) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SUN2, FRIGG, KIAA0668, RAB5IP, UNC84B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UH99 |
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#2: Protein/peptide | Mass: 3743.084 Da / Num. of mol.: 1 / Fragment: UNP residues 8769-8797 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SYNE1, C6orf98, KIAA0796, KIAA1262, KIAA1756, MYNE1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NF91 |
#3: Sugar | ChemComp-DMU / |
#4: Chemical | ChemComp-K / |
#5: 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: 2.99 Å3/Da / Density % sol: 58.91 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES, PH 7.5, 0.2 M ammonium acetate, 0.30% DM, 25% 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 20, 2011 |
Radiation | Monochromator: SINGLE CRYSTAL SI(220) SIDE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→85.5 Å / Num. obs: 13944 / % possible obs: 99.6 % / Observed criterion σ(I): 1.5 / Redundancy: 3.5 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.707 / Mean I/σ(I) obs: 1.5 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4DXT Resolution: 2.32→46.95 Å / SU ML: 0.26 / σ(F): 1.33 / Phase error: 22.89 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.48 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.273 Å2
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Refinement step | Cycle: LAST / Resolution: 2.32→46.95 Å
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Refine LS restraints |
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