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- PDB-5ed8: Crystal structure of CC2-SUN of mouse SUN2 -

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Basic information

Entry
Database: PDB / ID: 5ed8
TitleCrystal structure of CC2-SUN of mouse SUN2
ComponentsMKIAA0668 protein
KeywordsTRANSPORT PROTEIN / SUN domain / nuclear membrane
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 ...: / 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 2 / 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-like domain superfamily
Similarity search - Domain/homology
MKIAA0668 protein / SUN domain-containing protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 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: MKIAA0668 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0752
Polymers30,0511
Non-polymers241
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12800 Å2
Unit cell
Length a, b, c (Å)63.374, 63.374, 192.786
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein MKIAA0668 protein


Mass: 30050.902 Da / Num. of mol.: 1 / Fragment: UNP residues 433-694
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: mKIAA0668 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6A022, UniProt: Q8BJS4*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 3.53 Å3/Da / Density % sol: 65.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: 1.4M Na2HPO4/ KH2PO4 / PH range: 6.4-7.3

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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: Feb 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 14373 / % possible obs: 99.5 % / Redundancy: 4.3 % / Rsym value: 0.077 / Net I/σ(I): 21.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4 % / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
HKL-2000data collection
SHELXCDphasing
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.5→32.94 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2545 670 4.92 %
Rwork0.2136 12940 -
obs0.2157 13610 94.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 164.72 Å2 / Biso min: 37.99 Å2
Refinement stepCycle: final / Resolution: 2.5→32.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1870 0 1 76 1947
Biso mean--42.95 71.24 -
Num. residues----245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031931
X-RAY DIFFRACTIONf_angle_d0.7292628
X-RAY DIFFRACTIONf_chiral_restr0.032290
X-RAY DIFFRACTIONf_plane_restr0.003345
X-RAY DIFFRACTIONf_dihedral_angle_d14.632692
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5002-2.69320.35361320.2988226486
2.6932-2.9640.34471500.2686249794
2.964-3.39250.24121300.2177261297
3.3925-4.27280.2191240.1954270498
4.27280.24291340.2032286398
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
17.91392.29163.05224.249-1.10643.7478-0.36490.408-0.5173-0.25210.31691.27421.1361-1.25080.05960.6354-0.13680.01061.2346-0.31980.9949Chain A group 148.046425.029588.0383
24.36770.4177-3.99891.3592-0.18778.13160.38690.246-0.775-0.6031-0.19920.49670.3414-0.0069-0.14420.3677-0.0569-0.03590.5958-0.19560.5326Chain A group 249.177422.926875.0975
36.16860.3028-0.40096.02530.00297.21440.1567-0.0271-0.2379-0.01250.01360.15050.1903-0.0663-0.15520.2283-0.0246-0.0470.4075-0.05120.3166Chain A group 353.774118.165859.0268
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 454 through 499 )A
2X-RAY DIFFRACTION2chain 'A' and (resid 500 through 574 )A
3X-RAY DIFFRACTION3chain 'A' and (resid 575 through 698 )A

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