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- PDB-4dxt: Human SUN2 (AA 522-717) -

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Basic information

Entry
Database: PDB / ID: 4dxt
TitleHuman SUN2 (AA 522-717)
ComponentsSUN domain-containing protein 2
KeywordsSTRUCTURAL 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 / 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
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 / Galactose-binding domain-like / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / SUN domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.22 Å
AuthorsSosa, B. / Schwartz, T.U.
CitationJournal: 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
DepositionFeb 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SUN domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1762
Polymers22,1371
Non-polymers391
Water2,036113
1
A: SUN domain-containing protein 2
hetero molecules

A: SUN domain-containing protein 2
hetero molecules

A: SUN domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5286
Polymers66,4103
Non-polymers1173
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area7850 Å2
ΔGint-49 kcal/mol
Surface area27430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.580, 79.580, 199.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1148-

HOH

21A-1169-

HOH

31A-1194-

HOH

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Components

#1: Protein SUN domain-containing protein 2 / Protein unc-84 homolog B / Rab5-interacting protein / Rab5IP / Sad1/unc-84 protein-like 2


Mass: 22136.816 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
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.74 Å3/Da / Density % sol: 55.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 16% PEG3350, 0.2 M potassium thiocyanate, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2010
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→56.7 Å / Num. obs: 12305 / % possible obs: 99.8 % / Observed criterion σ(I): 3.5 / Redundancy: 5.9 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 20
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCdata collection
PHENIX(phenix.refine: dev_975)refinement
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.22→56.66 Å / SU ML: 0.34 / σ(F): 1.36 / Phase error: 23.92 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflection
Rfree0.226 1250 10.2 %
Rwork0.169 --
obs0.175 12305 99.7 %
all-12330 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.87 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 51.694 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20.41 Å20 Å2
2--0.83 Å20 Å2
3----1.24 Å2
Refinement stepCycle: LAST / Resolution: 2.22→56.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1565 0 1 113 1679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171646
X-RAY DIFFRACTIONf_angle_d1.9142255
X-RAY DIFFRACTIONf_dihedral_angle_d15.757598
X-RAY DIFFRACTIONf_chiral_restr0.127243
X-RAY DIFFRACTIONf_plane_restr0.011300

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