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- PDB-6tyt: Structure of Ku80 von Willebrand domain S229A mutant complexed wi... -

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Basic information

Entry
Database: PDB / ID: 6tyt
TitleStructure of Ku80 von Willebrand domain S229A mutant complexed with APLF and XLF Ku Binding Motif
Components
  • ALA-LYS-GLY-LEU-PHE-MET
  • ARG-LYS-ARG-ILE-LEU-PRO-THR-TRP-MET-LEU-ALA
  • X-ray repair cross-complementing protein 5
KeywordsDNA BINDING PROTEIN / Ku80 von Willebrand factor A domain / Fluorine-19 NMR / Ku binding motif / Conditional binding site
Function / homology
Function and homology information


ADP-D-ribose modification-dependent protein binding / regulation of isotype switching / histone chaperone activity / Ku70:Ku80 complex / poly-ADP-D-ribose binding / positive regulation of DNA ligation / regulation of epithelial to mesenchymal transition / single strand break repair / DNA repair-dependent chromatin remodeling / telomeric DNA binding ...ADP-D-ribose modification-dependent protein binding / regulation of isotype switching / histone chaperone activity / Ku70:Ku80 complex / poly-ADP-D-ribose binding / positive regulation of DNA ligation / regulation of epithelial to mesenchymal transition / single strand break repair / DNA repair-dependent chromatin remodeling / telomeric DNA binding / site of DNA damage / protein folding chaperone / DNA helicase activity / protein localization to chromatin / DNA-(apurinic or apyrimidinic site) endonuclease activity / 3'-5' exonuclease activity / embryo implantation / telomere maintenance / DNA endonuclease activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / double-strand break repair via nonhomologous end joining / double-strand break repair / site of double-strand break / histone binding / DNA recombination / damaged DNA binding / Hydrolases; Acting on ester bonds / hydrolase activity / DNA repair / nucleotide binding / DNA damage response / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol
Similarity search - Function
Aprataxin and PNK-like factor, PBZ domain / Aprataxin and PNK-like factor / PBZ domain / XLF, N-terminal / XLF N-terminal domain / PNK, FHA domain / FHA domain / XRCC4-like, N-terminal domain superfamily / Ku, C-terminal / Ku, C-terminal domain superfamily ...Aprataxin and PNK-like factor, PBZ domain / Aprataxin and PNK-like factor / PBZ domain / XLF, N-terminal / XLF N-terminal domain / PNK, FHA domain / FHA domain / XRCC4-like, N-terminal domain superfamily / Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Ku80 / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 beta-barrel domain / Ku70/Ku80 C-terminal arm / Ku70/Ku80 N-terminal alpha/beta domain / Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen / Ku70/Ku80 beta-barrel domain / SPOC-like, C-terminal domain superfamily / SMAD/FHA domain superfamily / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
non-homologous end-joining factor 1 isoform X1 / X-ray repair cross-complementing protein 5 / Aprataxin and PNK-like factor
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.40348787647 Å
AuthorsMin, J. / Pedersen, L.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIA-ES102645 United States
CitationJournal: DNA Repair (Amst.) / Year: 2019
Title: Ligand binding characteristics of the Ku80 von Willebrand domain.
Authors: Kim, K. / Min, J. / Kirby, T.W. / Gabel, S.A. / Pedersen, L.C. / London, R.E.
History
DepositionAug 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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: X-ray repair cross-complementing protein 5
B: ALA-LYS-GLY-LEU-PHE-MET
C: ARG-LYS-ARG-ILE-LEU-PRO-THR-TRP-MET-LEU-ALA


Theoretical massNumber of molelcules
Total (without water)30,0573
Polymers30,0573
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-10 kcal/mol
Surface area9920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.642, 79.407, 146.174
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein X-ray repair cross-complementing protein 5


Mass: 26169.980 Da / Num. of mol.: 1 / Fragment: Ku80 von Willebrand domain / Mutation: C190S, S229A, deletion loop (E171 through R188)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: XELAEV_18044412mg / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1L8EVE5, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein/peptide ALA-LYS-GLY-LEU-PHE-MET


Mass: 1918.394 Da / Num. of mol.: 1 / Fragment: XLF Ku Binding Motif / Source method: obtained synthetically / Source: (synth.) Xenopus laevis (African clawed frog) / References: UniProt: A0A1L8ENT6*PLUS
#3: Protein/peptide ARG-LYS-ARG-ILE-LEU-PRO-THR-TRP-MET-LEU-ALA


Mass: 1968.368 Da / Num. of mol.: 1 / Fragment: APLF Ku Binding Motif / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8IW19*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 1.99 Å3/Da / Density % sol: 38.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES NaOH pH 7.5, 25 % (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jun 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 10611 / % possible obs: 97 % / Redundancy: 5.7 % / Biso Wilson estimate: 66.1879875512 Å2 / Rrim(I) all: 0.41 / Net I/σ(I): 43
Reflection shellResolution: 2.35→2.39 Å / Num. unique obs: 410 / Rrim(I) all: 0.643

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TYZ

6tyz


Resolution: 2.40348787647→34.888011588 Å / SU ML: 0.361225211007 / Cross valid method: FREE R-VALUE / σ(F): 1.36284228671 / Phase error: 34.9799203314
RfactorNum. reflection% reflection
Rfree0.259533479025 488 4.94878815536 %
Rwork0.22504942686 --
obs0.226705772622 9861 96.0830166618 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 83.3805343643 Å2
Refinement stepCycle: LAST / Resolution: 2.40348787647→34.888011588 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1641 0 0 4 1645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001822041398661665
X-RAY DIFFRACTIONf_angle_d0.378013571632258
X-RAY DIFFRACTIONf_chiral_restr0.0385994338424278
X-RAY DIFFRACTIONf_plane_restr0.00109721775406286
X-RAY DIFFRACTIONf_dihedral_angle_d11.2031700419572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4035-2.48940.342557961643410.316793255799774X-RAY DIFFRACTION82.406471183
2.4894-2.5890.319465416535460.2879210862864X-RAY DIFFRACTION90.099009901
2.589-2.70680.44047996420.268121223863899X-RAY DIFFRACTION92.9841897233
2.7068-2.84940.307134787627510.293965440295947X-RAY DIFFRACTION98.5192497532
2.8494-3.02790.345851702856470.319218940516974X-RAY DIFFRACTION99.70703125
3.0279-3.26150.332190516829530.269989538707956X-RAY DIFFRACTION100
3.2615-3.58940.23068151479500.249411828414969X-RAY DIFFRACTION99.8041136141
3.5894-4.10810.219770128153540.232207749547976X-RAY DIFFRACTION99.5169082126
4.1081-5.17310.232903878838510.170339641266966X-RAY DIFFRACTION97.7884615385
5.1731-34.880.2504397053530.2017244322221048X-RAY DIFFRACTION99.2786293959
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)
16.7846391242-1.032569408370.5268881739020.357733614496-0.946365313846.51103397442-0.3185235125930.6065018550171.42924420989-0.2150730262350.1163641498130.248215064597-0.6158817711410.05514065276270.09741570962840.595802283404-0.1002040737030.0009087645797740.5844091901930.0172247804720.65989523233916.40411419569.51088032021-24.995785096
26.20940326467-1.16283290837-3.469586814423.327596275921.878772709718.89736303609-0.1937472502190.382493919970.579411786885-0.3245496056610.05154037867210.651153198267-0.388704005773-1.264883935670.1964481604680.565959186208-0.0180627329125-0.1622066941170.772153462848-0.004995830231220.6466659244174.102597566718.7564983175-24.6855851421
31.84319801557-0.511660779510.7974701852421.82178314351-0.8012954846870.827055576925-0.578045486811-0.074633031556-0.798120379383-0.6335791940090.0234187933983-0.05899888796660.787723867877-0.621203220246-0.02250595987030.69262757324-0.2370392244390.04812082468310.522888250454-0.2223294110270.7757523038725.86091125379-4.18556687217-22.3625165578
49.1327046910.4477724412890.06520874711711.22293431655-0.1532924958387.42202725852-0.289236628664-1.325307850540.7676277343840.4756174196270.1641275146280.811022062227-0.290994317429-1.307326380890.1144220359750.598682512590.0846696062987-0.02875060609240.781184364139-0.162225243860.4738113299924.217633595216.17707497847-8.56178297705
54.254689142510.639703682310.6650102171083.5289892809-1.193295338538.94350000337-0.3452184944070.385077554930.3762627910540.02895851807410.4094569824640.189425960156-0.6202279009690.306599961661-0.2172599857460.660844915862-0.09974105190840.05391183214050.698332675621-0.150460416310.65852824527216.27473761126.64741272198-12.352973635
66.296413313811.66038570238-2.565427838141.28347648346-0.9132136205368.71436503667-0.566897408155-0.507669008389-0.4905334600330.0582663267207-0.372794185963-0.1028178044990.04696306024220.8257693173540.8476157704460.601919452049-0.048306648942-0.04254498826470.643519471255-0.05453004153750.65235152599918.34298231164.25612786551-11.1922223751
75.732934594415.73008471483-4.939500567215.72655138905-4.937934279334.25653682586-1.199721623941.91655329555-2.71898656449-1.28196876913-0.06128768344180.5896569729882.187626799-0.2829031416740.08756228448810.8317161675150.1682820759580.1396342680510.822757416095-0.3187007865640.742040363318.4699317049-4.67599770004-20.3937251572
87.917141579288.987639644845.491280702351.999825557566.23321771183.8069991147-0.6283435868731.158242622852.562663010630.437568371637-0.3380820227051.12700457408-0.194445034139-1.953682642620.6930423436250.5853048681730.105241256505-0.05515768806961.04102582152-0.1121810263310.862198592397-5.616191579058.75425507699-9.41867326095
98.557813617082.86318891758-5.216592638635.778767764072.696832899057.275797508370.539745845092-0.629250136946-1.609100222670.298509037802-2.016581255651.78845193588-0.150655894031-0.3296679983441.55328452910.610162608549-0.1806845985180.1172071545971.43089823567-0.3061622921361.13734315162-7.25928297396-1.31171100109-12.2191217591
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 120 )
3X-RAY DIFFRACTION3chain 'A' and (resid 121 through 134 )
4X-RAY DIFFRACTION4chain 'A' and (resid 135 through 156 )
5X-RAY DIFFRACTION5chain 'A' and (resid 157 through 197 )
6X-RAY DIFFRACTION6chain 'A' and (resid 198 through 236 )
7X-RAY DIFFRACTION7chain 'B' and (resid 306 through 311 )
8X-RAY DIFFRACTION8chain 'C' and (resid 182 through 187 )
9X-RAY DIFFRACTION9chain 'C' and (resid 188 through 192 )

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