+Open data
-Basic information
Entry | Database: PDB / ID: 4dxs | ||||||
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Title | Human SUN2-KASH2 complex | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / beta-sandwich / LINC complex | ||||||
Function / homology | Function and homology information 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 / regulation of cilium assembly / lamin binding / nuclear lumen / filopodium membrane / nuclear outer membrane ...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 / regulation of cilium assembly / lamin binding / nuclear lumen / filopodium membrane / nuclear outer membrane / nuclear migration / nuclear inner membrane / intermediate filament cytoskeleton / centrosome localization / lamellipodium membrane / protein-membrane adaptor activity / sarcoplasmic reticulum membrane / Meiotic synapsis / mitotic spindle organization / meiotic cell cycle / sarcoplasmic reticulum / condensed nuclear chromosome / Z disc / nuclear envelope / actin binding / microtubule binding / nuclear membrane / chromosome, telomeric region / endosome membrane / positive regulation of cell migration / focal adhesion / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 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 | 4dxs.cif.gz | 61.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dxs.ent.gz | 43 KB | Display | PDB format |
PDBx/mmJSON format | 4dxs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/4dxs ftp://data.pdbj.org/pub/pdb/validation_reports/dx/4dxs | HTTPS FTP |
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-Related structure data
Related structure data | 4dxrC 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
#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: 3785.054 Da / Num. of mol.: 1 / Fragment: UNP residues 6857-6885 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SYNE2, KIAA1011, NUA / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WXH0 |
#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: 3 Å3/Da / Density % sol: 59.07 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.1 M HEPES, pH 7.4, 7% PEG4000, 10% 1,6-hexanediol, 0.25% DM, 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: Jul 15, 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: 2.7→43.3 Å / Num. obs: 8912 / % possible obs: 99.8 % / Observed criterion σ(I): 2.7 / Redundancy: 5.9 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 2.7 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4DXT Resolution: 2.71→36.06 Å / SU ML: 0.42 / σ(F): 1.35 / Phase error: 26.67 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.18 Å2 / ksol: 0.32 e/Å3 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.531 Å2
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Refinement step | Cycle: LAST / Resolution: 2.71→36.06 Å
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Refine LS restraints |
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