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- PDB-6wme: Human Sun2-KASH3 complex -

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Basic information

Entry
Database: PDB / ID: 6wme
TitleHuman Sun2-KASH3 complex
Components
  • Nesprin-3
  • SUN domain-containing protein 2
KeywordsSTRUCTURAL PROTEIN / 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 / establishment of protein localization to membrane / nuclear outer membrane / nuclear migration / nuclear inner 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 / lamin binding / establishment of protein localization to membrane / nuclear outer membrane / nuclear migration / nuclear inner membrane / centrosome localization / rough endoplasmic reticulum / protein-membrane adaptor activity / cytoskeleton organization / Meiotic synapsis / mitotic spindle organization / meiotic cell cycle / condensed nuclear chromosome / actin filament binding / nuclear envelope / regulation of cell shape / microtubule binding / nuclear membrane / membrane => GO:0016020 / chromosome, telomeric region / endosome membrane / positive regulation of cell migration / identical protein binding / membrane / cytoplasm
Similarity search - Function
Nesprin-3 / 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 ...Nesprin-3 / 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 / Spectrin repeats
Similarity search - Domain/homology
: / Nesprin-3 / SUN domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsCruz, V.E. / Schwartz, T.U.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)AR065484 United States
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Structural Analysis of Different LINC Complexes Reveals Distinct Binding Modes.
Authors: Cruz, V.E. / Esra Demircioglu, F. / Schwartz, T.U.
History
DepositionApr 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0063
Polymers25,9672
Non-polymers391
Water4,378243
1
A: SUN domain-containing protein 2
B: Nesprin-3
hetero molecules

A: SUN domain-containing protein 2
B: Nesprin-3
hetero molecules

A: SUN domain-containing protein 2
B: Nesprin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0189
Polymers77,9016
Non-polymers1173
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_875-y+3,x-y+2,z1
crystal symmetry operation3_685-x+y+1,-x+3,z1
Buried area13480 Å2
ΔGint-76 kcal/mol
Surface area27320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.709, 78.709, 173.278
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-1035-

HOH

21A-1120-

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: 22349.930 Da / Num. of mol.: 1 / Mutation: Q534D, L574I, T683G, M684R, A685G
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-3 / KASH domain-containing protein 3 / KASH3 / Nuclear envelope spectrin repeat protein 3


Mass: 3616.972 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYNE3, C14orf139, C14orf49, LINC00341 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6ZMZ3
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.99 Å3/Da / Density % sol: 58.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16-18% PEG 3350, 0.2M magnesium chloride, 0.1M ammonium citrate, 0.1M BisTris/HCl, 0.01M nickel chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.53→63.43 Å / Num. obs: 47679 / % possible obs: 99.9 % / Redundancy: 20 % / Biso Wilson estimate: 27.71 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.014 / Net I/σ(I): 68.3
Reflection shellResolution: 1.53→1.57 Å / Num. unique obs: 2783 / CC1/2: 0.753 / % possible all: 82

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DXT

4dxt


Resolution: 1.53→63.43 Å / SU ML: 0.1972 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.9494
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2449 1993 4.18 %
Rwork0.2094 45686 -
obs0.2108 47679 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.42 Å2
Refinement stepCycle: LAST / Resolution: 1.53→63.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1661 0 1 244 1906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621789
X-RAY DIFFRACTIONf_angle_d1.05622443
X-RAY DIFFRACTIONf_chiral_restr0.0616263
X-RAY DIFFRACTIONf_plane_restr0.0063323
X-RAY DIFFRACTIONf_dihedral_angle_d28.8479247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.570.4081150.3942658X-RAY DIFFRACTION82.14
1.57-1.620.32361410.31063225X-RAY DIFFRACTION99.64
1.62-1.660.29071410.27373230X-RAY DIFFRACTION99.73
1.66-1.720.26521420.25033251X-RAY DIFFRACTION99.85
1.72-1.780.26061410.22983245X-RAY DIFFRACTION99.85
1.78-1.850.251420.22243238X-RAY DIFFRACTION99.91
1.85-1.930.25531430.22973278X-RAY DIFFRACTION99.85
1.93-2.030.25841430.21033266X-RAY DIFFRACTION99.88
2.03-2.160.24911430.20733288X-RAY DIFFRACTION100
2.16-2.330.22311440.21053300X-RAY DIFFRACTION99.94
2.33-2.560.22661450.20983322X-RAY DIFFRACTION99.86
2.56-2.930.24641460.2073351X-RAY DIFFRACTION99.97
2.94-3.70.25681480.19543399X-RAY DIFFRACTION99.92
3.7-63.430.23071590.20123635X-RAY DIFFRACTION99.84
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)Origin x (Å)Origin y (Å)Origin z (Å)
11.870264677020.315517576679-0.9736633587711.7044732475-2.289458406669.698302125790.1815580952970.18011306190.0473339840967-0.02666738671260.1214242226090.248492845669-0.395794148823-0.824064899968-0.3120261295980.2145952648730.0257427053131-0.003257538305980.2337832481510.01146722207240.30192503845633.5878376041115.518484511-8.57189651298
21.21937615654-0.0531336490051-0.05303376552280.696700182105-0.01311820826621.336002306460.0379586543045-0.1791443664180.03153068424160.1206364808540.0810136732823-0.09777538161440.2091845019240.0120093193716-0.1275085280140.263087637319-0.028962419227-0.05285440957680.193092857392-0.009534459580270.23910387973835.7407432274100.5936458623.1184985085
32.311000385120.3544359276830.6816375602391.29258414624-0.1650718310591.576082841750.06419178829680.0932515438157-0.243614899388-0.06226361044420.1011474063840.01118856008990.51070461237-0.169885832543-0.1445512995030.410023942527-0.0635515819851-0.08807790462920.240850893978-0.01507827943410.28705867434531.341367199992.894037480410.9125751465
42.13856973907-0.630424056367-0.7290220491961.566701156450.5334929359071.334065738090.1240182365460.124282237613-0.354849280582-0.123467982826-0.01132017412080.22545203420.390014401254-0.318515819517-0.1373739240180.317953778386-0.0924402279331-0.08279093623290.2413014499080.005159462590370.24887886452827.308793628393.203648463213.3417542874
51.15769887885-1.10369633789-0.5933070290841.1601878479-0.312357329433.7438208119-0.0709255236710.459079921434-0.632166331477-0.4443822199540.02828164333050.3265904954820.747073991035-0.446169909367-0.03969234766480.28078028682-0.0926898247913-0.01906430202250.3772617476-0.106678039120.44590523415550.9587451175122.03983796836.1986441287
63.41202607528-1.94286773314-2.680296855698.8403340054.306724295544.176280574520.122710445503-0.02701773392750.08559756473930.202652860165-0.0932842658928-0.225373046256-0.118193315660.729178252176-0.1229595511340.265289978788-0.0203840142935-0.01225414667340.3239467985540.004393187873550.20243604740651.2890694484110.04915751731.1160766675
73.358046332491.663345683042.169066971832.015445051312.137370197092.420369775960.328402316437-0.0538615447686-0.5509602446170.1281705907380.248926895905-0.3122035407930.4863844515950.172665951887-0.3304800141750.2779544543840.0778367661741-0.07500780919750.275838387419-0.06116258009830.30403165714651.124379063398.258852483423.3109154623
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 522 through 540 )
2X-RAY DIFFRACTION2chain 'A' and (resid 541 through 618 )
3X-RAY DIFFRACTION3chain 'A' and (resid 619 through 678 )
4X-RAY DIFFRACTION4chain 'A' and (resid 679 through 716 )
5X-RAY DIFFRACTION5chain 'B' and (resid 960 through 963 )
6X-RAY DIFFRACTION6chain 'B' and (resid 964 through 968 )
7X-RAY DIFFRACTION7chain 'B' and (resid 969 through 975 )

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