+Open data
-Basic information
Entry | Database: PDB / ID: 6wmg | ||||||
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Title | Human Sun2 (500-717) | ||||||
Components | SUN domain-containing protein 2 | ||||||
Keywords | STRUCTURAL PROTEIN / 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 / lamin binding / nuclear migration / nuclear inner membrane / centrosome localization / protein-membrane adaptor activity ...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 / lamin binding / nuclear migration / nuclear inner membrane / centrosome localization / protein-membrane adaptor activity / Meiotic synapsis / mitotic spindle organization / meiotic cell cycle / condensed nuclear chromosome / nuclear envelope / microtubule binding / nuclear membrane / chromosome, telomeric region / endosome membrane / positive regulation of cell migration / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Cruz, V.E. / Schwartz, T.U. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2020 Title: Structural Analysis of Different LINC Complexes Reveals Distinct Binding Modes. Authors: Cruz, V.E. / Esra Demircioglu, F. / 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 | 6wmg.cif.gz | 115.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wmg.ent.gz | 73.4 KB | Display | PDB format |
PDBx/mmJSON format | 6wmg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/6wmg ftp://data.pdbj.org/pub/pdb/validation_reports/wm/6wmg | HTTPS FTP |
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-Related structure data
Related structure data | 6wmdC 6wmeC 6wmfC 4dxtS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 24637.617 Da / Num. of mol.: 1 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: Chemical | ChemComp-K / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.65 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 14.5% PEG 3350, 0.2M sodium bromide, 0.1M potassium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→56.51 Å / Num. obs: 19072 / % possible obs: 99 % / Redundancy: 3.7 % / Biso Wilson estimate: 37.45 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.042 / Net I/σ(I): 24 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1319 / CC1/2: 0.652 / Rpim(I) all: 0.599 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DXT Resolution: 1.9→56.51 Å / SU ML: 0.2182 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.8269
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.11 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→56.51 Å
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Refine LS restraints |
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LS refinement shell |
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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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