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- PDB-4dxs: Human SUN2-KASH2 complex -

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Basic information

Entry
Database: PDB / ID: 4dxs
TitleHuman SUN2-KASH2 complex
Components
  • Nesprin-2
  • SUN 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 / cytoskeleton-nuclear membrane anchor activity / meiotic nuclear membrane microtubule tethering complex / regulation of cilium assembly / intermediate filament cytoskeleton / nuclear outer membrane / nuclear lumen / filopodium membrane / centrosome localization ...nuclear migration along microfilament / nucleokinesis involved in cell motility in cerebral cortex radial glia guided migration / cytoskeleton-nuclear membrane anchor activity / meiotic nuclear membrane microtubule tethering complex / regulation of cilium assembly / intermediate filament cytoskeleton / nuclear outer membrane / nuclear lumen / filopodium membrane / centrosome localization / nuclear migration / lamellipodium membrane / sarcoplasmic reticulum membrane / Meiotic synapsis / sarcoplasmic reticulum / Z disc / fibrillar center / nuclear envelope / actin binding / nuclear membrane / cilium / positive regulation of cell migration / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / focal adhesion / mitochondrion / extracellular exosome / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
KASH domain / Nuclear envelope localisation domain / KASH domain profile. / Nuclear envelope localisation domain / Sad1 / UNC-like C-terminal / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Actinin-type actin-binding domain signature 1. ...KASH domain / Nuclear envelope localisation domain / KASH domain profile. / Nuclear envelope localisation domain / Sad1 / UNC-like C-terminal / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / 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 / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S21 / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Nesprin-2 / Small ribosomal subunit protein bS21
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 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
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: Nesprin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7024
Polymers26,1802
Non-polymers5222
Water73941
1
A: SUN domain-containing protein 2
B: Nesprin-2
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)80,10512
Polymers78,5406
Non-polymers1,5656
Water1086
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 area16480 Å2
ΔGint-83 kcal/mol
Surface area27720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.320, 79.320, 260.030
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: 22395.053 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: 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: 3785.054 Da / Num. of mol.: 1 / Fragment: UNP residues 6857-6885
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYNE2, KIAA1011, NUA / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WXH0
#3: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM
#4: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 59.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1 M HEPES, pH 7.4, 7% PEG4000, 10% 1,6-hexanediol, 0.25% DM, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2011
RadiationMonochromator: SINGLE CRYSTAL SI(220) SIDE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→43.3 Å / Num. obs: 8912 / % possible obs: 99.8 % / Observed criterion σ(I): 2.7 / Redundancy: 5.9 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 21
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 2.7 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCdata collection
PHENIX(phenix.refine: dev_975)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DXT

4dxt


Resolution: 2.71→36.06 Å / SU ML: 0.42 / σ(F): 1.35 / Phase error: 26.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.241 891 10 %
Rwork0.182 --
obs0.188 8909 99.9 %
all-8930 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.18 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 65.531 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å2-0.43 Å20 Å2
2---0.85 Å20 Å2
3---1.28 Å2
Refinement stepCycle: LAST / Resolution: 2.71→36.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1746 0 26 41 1813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131825
X-RAY DIFFRACTIONf_angle_d1.7322492
X-RAY DIFFRACTIONf_dihedral_angle_d14.898654
X-RAY DIFFRACTIONf_chiral_restr0.116274
X-RAY DIFFRACTIONf_plane_restr0.0081416

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