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- PDB-6wmf: Human Sun2-KASH5 complex -

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Basic information

Entry
Database: PDB / ID: 6wmf
TitleHuman Sun2-KASH5 complex
Components
  • Protein KASH5
  • SUN domain-containing protein 2
KeywordsSTRUCTURAL PROTEIN / LINC Complex
Function / homology
Function and homology information


telomere localization / : / chromosome localization to nuclear envelope involved in homologous chromosome segregation / 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 / spindle localization / meiotic spindle pole / meiotic nuclear membrane microtubule tethering complex ...telomere localization / : / chromosome localization to nuclear envelope involved in homologous chromosome segregation / 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 / spindle localization / meiotic spindle pole / meiotic nuclear membrane microtubule tethering complex / homologous chromosome pairing at meiosis / lateral element / lamin binding / nuclear outer membrane / nuclear migration / nuclear inner membrane / centrosome localization / dynein complex binding / oogenesis / spindle assembly / protein-membrane adaptor activity / Meiotic synapsis / mitotic spindle organization / meiotic cell cycle / condensed nuclear chromosome / actin filament organization / double-strand break repair via homologous recombination / nuclear envelope / spermatogenesis / microtubule binding / nuclear membrane / chromosome, telomeric region / endosome membrane / positive regulation of cell migration / identical protein binding
Similarity search - Function
KASH5-like coiled-coil domain / Protein KASH5 / Protein KASH5, EF-hand-like domain / EF-hand domain / Coiled-coil region of CCDC155 or KASH / SUN domain-containing protein 1-5 / SUN coiled coil domain 2 / SUN2 helix-turn-helix domain / SUN domain profile. / SUN domain ...KASH5-like coiled-coil domain / Protein KASH5 / Protein KASH5, EF-hand-like domain / EF-hand domain / Coiled-coil region of CCDC155 or KASH / 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 / EF-hand domain pair
Similarity search - Domain/homology
: / Protein KASH5 / SUN domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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: Protein KASH5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1583
Polymers25,1192
Non-polymers391
Water19811
1
A: SUN domain-containing protein 2
B: Protein KASH5
hetero molecules

A: SUN domain-containing protein 2
B: Protein KASH5
hetero molecules

A: SUN domain-containing protein 2
B: Protein KASH5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4759
Polymers75,3576
Non-polymers1173
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_785-y+2,x-y+3,z1
crystal symmetry operation3_475-x+y-1,-x+2,z1
Buried area12950 Å2
ΔGint-85 kcal/mol
Surface area25460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.435, 78.435, 249.441
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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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: 22381.025 Da / Num. of mol.: 1
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 Protein KASH5 / Coiled-coil domain-containing protein 155 / KASH domain-containing protein 5


Mass: 2738.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCDC155, KASH5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N6L0
#3: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.24 Å3/Da / Density % sol: 62.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 14% PEG3000, 0.1M BisTris/HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / 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: 2.6→83.15 Å / Num. obs: 9383 / % possible obs: 99.2 % / Redundancy: 15.9 % / Biso Wilson estimate: 79.34 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.025 / Net I/σ(I): 37.3
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1257 / CC1/2: 0.51 / Rpim(I) all: 0.466 / % possible all: 95

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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: 2.6→83.15 Å / SU ML: 0.5021 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.3665
RfactorNum. reflection% reflection
Rfree0.2859 938 10 %
Rwork0.2212 --
obs0.2278 9383 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 96.72 Å2
Refinement stepCycle: LAST / Resolution: 2.6→83.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1584 0 1 11 1596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00971628
X-RAY DIFFRACTIONf_angle_d1.21312222
X-RAY DIFFRACTIONf_chiral_restr0.0696247
X-RAY DIFFRACTIONf_plane_restr0.0076288
X-RAY DIFFRACTIONf_dihedral_angle_d22.2836216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.740.43531240.33361133X-RAY DIFFRACTION95.44
2.74-2.910.42491340.3251190X-RAY DIFFRACTION99.62
2.91-3.140.35221310.26471192X-RAY DIFFRACTION99.77
3.14-3.450.29571330.22971197X-RAY DIFFRACTION99.92
3.45-3.950.26091350.20551218X-RAY DIFFRACTION99.85
3.95-4.980.231370.18851219X-RAY DIFFRACTION99.85
4.98-83.150.29511440.21931296X-RAY DIFFRACTION99.93
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)
16.119375153144.12432795864-5.910717607792.78405770046-3.867331158655.802982060540.06606353903931.144680857410.7819103150350.07462029654380.3727297242730.71805878563-1.55985765375-3.026794497820.004999465573811.214206332290.0438941102625-0.1025342655231.090483617720.082840784490.697135728329-45.0826671881115.294489164240.964096418
24.865325510571.378125302641.777424271221.90421540570.606290062855.25476215590.563028853805-0.708273561619-0.4176911281810.120788242357-0.0645153628442-0.115595299931.21347724673-0.00204940434838-0.5228551774420.906669535980.0145878340038-0.02690476618570.7484043918120.04214783452650.535894814078-43.89235324100.897684196272.179201863
37.83823119845-1.475164083931.065700406393.47555961758-2.600389304528.92018793886-0.0349046490218-1.108684515490.1364668746830.419842519944-0.022773565392-0.147559158617-0.357835270241-0.09588607611880.01358872962570.754530589012-0.0267121497867-0.1104257071570.6084916965010.01291147319640.425925069135-39.540426067998.7861211805271.997921675
45.27281628925-1.16181996748-1.251439997473.952555005352.321376479882.19847527375-0.4268891431110.385630875735-0.04196075938670.3192296888610.3740498904320.2888760650960.564469568366-0.2602762128850.1972916464610.846631372443-0.0932631759721-0.1153648173870.6786926873590.05375499692640.369747317959-49.241565641897.8467108857263.136271863
52.03206946565-1.12347826282-4.125189310123.763923111251.655497798489.73005384166-0.883497672069-0.475529582817-1.325483157840.07647619522030.323523295099-0.1267538447921.5122936801-0.09140571207960.3414637151661.10464926659-0.00270618107108-0.1853061108280.5061567040380.1070721419940.708565311195-48.776263677290.0125524073265.092401989
67.17243687133-2.41301175099-0.3582240411935.46595086366-1.042766560825.110323603370.2423005729230.420115541232-0.827191917501-0.7530342747160.1222467201310.2674215648641.207628201810.252803757418-0.4087995074340.772791454238-0.0421320278444-0.09517317600440.684568092227-0.007821334861590.562773928582-46.940047341491.1551687725261.345767433
77.801575355643.857716439617.233508768347.569466979210.201142042969.342788220680.837291239757-0.9163245406381.219688668210.385947831036-0.8782685115280.4092278472250.126335713337-1.302722201260.5311075036990.7868553090570.1617845171430.02114278062150.974570736319-0.1241177597170.473422154171-56.4513306422101.720117479260.696397229
82.19589434747-0.7377534963990.7386499180935.314414205265.118445639235.700562223910.05808296422240.177978890789-0.4911884219411.553418105171.72202925513-2.317466217680.4639918752520.918831230179-1.247064088930.9227896429-0.100213269703-0.08654211753440.969690356335-0.08227992550890.703677495577-27.5396128268106.279118404277.62866563
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 581 )
3X-RAY DIFFRACTION3chain 'A' and (resid 582 through 608 )
4X-RAY DIFFRACTION4chain 'A' and (resid 609 through 634 )
5X-RAY DIFFRACTION5chain 'A' and (resid 635 through 659 )
6X-RAY DIFFRACTION6chain 'A' and (resid 660 through 707 )
7X-RAY DIFFRACTION7chain 'A' and (resid 708 through 717 )
8X-RAY DIFFRACTION8chain 'B' and (resid 783 through 797 )

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