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- PDB-5ed9: Crystal structure of CC1 of mouse SUN2 -

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Basic information

Entry
Database: PDB / ID: 5ed9
TitleCrystal structure of CC1 of mouse SUN2
ComponentsSUN domain-containing protein 2
KeywordsTRANSPORT PROTEIN / Coiled-coil
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 / nuclear envelope organization / lamin binding / 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 / nuclear envelope organization / lamin binding / nuclear inner membrane / centrosome localization / protein-membrane adaptor activity / meiotic cell cycle / condensed nuclear chromosome / nuclear envelope / nuclear membrane / chromosome, telomeric region / endosome membrane / positive regulation of cell migration / identical protein binding
Similarity search - Function
SUN domain-containing protein 1-5 / SUN coiled coil domain 2 / SUN2 helix-turn-helix domain / SUN domain profile. / SUN domain / Sad1 / UNC-like C-terminal
Similarity search - Domain/homology
SUN domain-containing protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.009 Å
AuthorsNie, S. / Ke, H.M. / Gao, F. / Ren, J.Q. / Wang, M.Z. / Huo, L. / Gong, W.M. / Feng, W.
CitationJournal: Structure / Year: 2016
Title: Coiled-Coil Domains of SUN Proteins as Intrinsic Dynamic Regulators
Authors: Nie, S. / Ke, H. / Gao, F. / Ren, J. / Wang, M. / Huo, L. / Gong, W. / Feng, W.
History
DepositionOct 21, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUN domain-containing protein 2
B: SUN domain-containing protein 2
C: SUN domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)25,8323
Polymers25,8323
Non-polymers00
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-65 kcal/mol
Surface area13470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.371, 34.743, 99.839
Angle α, β, γ (deg.)90.000, 101.490, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein SUN domain-containing protein 2 / Protein unc-84 homolog B / Sad1/unc-84 protein-like 2


Mass: 8610.674 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sun2, Unc84b / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BJS4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 61.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M Tris-HCl, 25%(w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 19246 / % possible obs: 98.6 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.163 / Net I/σ(I): 9.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.4 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC(phenix.refine: 1.8.2_1309)refinement
PDB_EXTRACT3.15data extraction
HKL-2000data collection
SHELXCDphasing
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.009→36.295 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2569 886 5.09 %
Rwork0.211 --
obs0.2134 17390 87.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.8 Å2 / Biso mean: 33.0262 Å2 / Biso min: 9.74 Å2
Refinement stepCycle: final / Resolution: 2.009→36.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1621 0 0 377 1998
Biso mean---29.13 -
Num. residues----206

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