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- PDB-4fi9: Structure of human SUN-KASH complex -

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Basic information

Entry
Database: PDB / ID: 4fi9
TitleStructure of human SUN-KASH complex
Components
  • Nesprin-2
  • SUN domain-containing protein 2
KeywordsPROTEIN BINDING / LINC complex / Transmembrane protein
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 / regulation of cilium assembly / nuclear lumen / lamin binding / filopodium membrane / nuclear outer membrane ...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 / regulation of cilium assembly / nuclear lumen / lamin binding / filopodium membrane / nuclear outer membrane / nuclear migration / nuclear inner membrane / intermediate filament cytoskeleton / centrosome localization / lamellipodium membrane / protein-membrane adaptor activity / sarcoplasmic reticulum membrane / Meiotic synapsis / mitotic spindle organization / condensed nuclear chromosome / sarcoplasmic reticulum / meiotic cell cycle / Z disc / nuclear envelope / actin binding / microtubule binding / nuclear membrane / chromosome, telomeric region / endosome membrane / positive regulation of cell migration / focal adhesion / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Nuclear anchorage protein 1-like / KASH domain / Nuclear envelope localisation domain / KASH domain profile. / Nuclear envelope localisation domain / SUN domain-containing protein 1-5 / SUN coiled coil domain 2 / SUN2 helix-turn-helix domain / SUN domain profile. / SUN domain ...Nuclear anchorage protein 1-like / KASH domain / Nuclear envelope localisation domain / KASH domain profile. / Nuclear envelope localisation domain / 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 / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Spectrin repeats / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Galactose-binding domain-like / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Nesprin-2 / SUN domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsWang, W.J. / Shi, Z.B.
CitationJournal: Cell Res. / Year: 2012
Title: Structural insights into SUN-KASH complexes across the nuclear envelope.
Authors: Wang, W. / Shi, Z. / Jiao, S. / Chen, C. / Wang, H. / Liu, G. / Wang, Q. / Zhao, Y. / Greene, M.I. / Zhou, Z.
History
DepositionJun 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,5812
Polymers23,5812
Non-polymers00
Water362
1
A: SUN domain-containing protein 2
B: Nesprin-2

A: SUN domain-containing protein 2
B: Nesprin-2

A: SUN domain-containing protein 2
B: Nesprin-2


Theoretical massNumber of molelcules
Total (without water)70,7426
Polymers70,7426
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area11010 Å2
ΔGint-65 kcal/mol
Surface area28180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.835, 79.835, 280.221
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: 21925.600 Da / Num. of mol.: 1 / Fragment: SUN domain (unp residues 523-717)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUN2, FRIGG, KIAA0668, RAB5IP, UNC84B / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9UH99
#2: Protein/peptide Nesprin-2 / Nuclear envelope spectrin repeat protein 2 / Nucleus and actin connecting element protein / Protein ...Nuclear envelope spectrin repeat protein 2 / Nucleus and actin connecting element protein / Protein NUANCE / Synaptic nuclear envelope protein 2 / Syne-2


Mass: 1654.905 Da / Num. of mol.: 1 / Fragment: KASH domain (unp residues 6872-6883) / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8WXH0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.64 Å3/Da / Density % sol: 66.25 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 50 mM MgCl2, 100 mM HEPES, 6% PEG5000 mme, 19.5 mM HECAMEG, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 8, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. all: 6908 / Num. obs: 6763 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 21.5
Reflection shellResolution: 3.05→3.1 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 3.5 / Num. unique all: 325 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→50 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.856 / SU B: 48.825 / SU ML: 0.411 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 30.103 / ESU R Free: 0.485 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31031 322 4.8 %RANDOM
Rwork0.24051 ---
obs0.24381 6421 97.55 %-
all-6582 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.194 Å2
Baniso -1Baniso -2Baniso -3
1--4.47 Å2-2.23 Å20 Å2
2---4.47 Å20 Å2
3---6.7 Å2
Refinement stepCycle: LAST / Resolution: 3.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1603 0 0 2 1605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211654
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.9382268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7815207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.18623.05672
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.09115223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.245159
X-RAY DIFFRACTIONr_chiral_restr0.1060.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0221303
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4121.51047
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.80321688
X-RAY DIFFRACTIONr_scbond_it1.0763607
X-RAY DIFFRACTIONr_scangle_it1.9284.5580
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.048→3.127 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 21 -
Rwork0.283 470 -
obs-470 98.59 %
Refinement TLS params.Method: refined / Origin x: -6.8124 Å / Origin y: -30.5801 Å / Origin z: -14.02 Å
111213212223313233
T0.1826 Å20.0763 Å2-0.0124 Å2-0.0161 Å20.0148 Å2--0.145 Å2
L2.7454 °2-0.0366 °20.601 °2-3.0235 °2-1.109 °2--3.8398 °2
S-0.0453 Å °0.4489 Å °0.274 Å °-0.2742 Å °0.0577 Å °0.0951 Å °-0.5532 Å °-0.1881 Å °-0.0124 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A523 - 717
2X-RAY DIFFRACTION1A801 - 802

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