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- PDB-3unp: Structure of human SUN2 SUN domain -

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Basic information

Entry
Database: PDB / ID: 3unp
TitleStructure of human SUN2 SUN domain
ComponentsSUN domain-containing protein 2
KeywordsTRANSPORT PROTEIN / trimer / nuclear envelope / SUN domain / KASH domain / LINC complex / nuclear migration
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
ACETYL GROUP / SUN domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.39 Å
AuthorsZhou, Z.C. / Greene, M.I.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structure of Sad1-UNC84 homology (SUN) domain defines features of molecular bridge in nuclear envelope
Authors: Zhou, Z.C. / Du, X. / Cai, Z. / Song, X. / Zhang, H. / Mizuno, T. / Suzuki, E. / Yee, M.R. / Berezov, A. / Murali, R. / Wu, S.-L. / Karger, B.L. / Greene, M.I. / Wang, Q.
History
DepositionNov 16, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: 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 / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)22,9302
Polymers22,8861
Non-polymers441
Water1,06359
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)68,7896
Polymers68,6573
Non-polymers1323
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area6090 Å2
ΔGint-39 kcal/mol
Surface area26180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.918, 78.918, 197.918
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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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: 22885.674 Da / Num. of mol.: 1 / Fragment: SUN domain, residues 520-717
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUN2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UH99
#2: Chemical ChemComp-ACE / ACETYL GROUP / Acetyl group


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.59 Å3/Da / Density % sol: 52.53 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M imidazole, 1.0M sodium acetate, 10 mM YCl3, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. all: 11047 / Num. obs: 11047 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0
Reflection shellResolution: 2.85→2.95 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SOLVEphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.39→39.47 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.903 / SU B: 8.048 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2664 967 10.3 %RANDOM
Rwork0.2183 ---
all0.22331 8685 --
obs0.22331 8425 96.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.261 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20.15 Å20 Å2
2--0.3 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.39→39.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1479 0 3 59 1541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0221524
X-RAY DIFFRACTIONr_angle_refined_deg2.6681.932080
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.4535191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94223.33369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg26.39315215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.483159
X-RAY DIFFRACTIONr_chiral_restr0.2240.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021196
X-RAY DIFFRACTIONr_nbd_refined0.3020.2709
X-RAY DIFFRACTIONr_nbtor_refined0.3430.2989
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2680.275
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5180.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3320.23
X-RAY DIFFRACTIONr_mcbond_it1.8261.5981
X-RAY DIFFRACTIONr_mcangle_it2.76121546
X-RAY DIFFRACTIONr_scbond_it3.4743614
X-RAY DIFFRACTIONr_scangle_it4.9554.5534
LS refinement shellResolution: 2.393→2.454 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 56 -
Rwork0.26 531 -
obs--84.58 %

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