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- PDB-6tyz: Structure of Ku80 von Willebrand domain complexed with APLF Ku Bi... -

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Basic information

Entry
Database: PDB / ID: 6tyz
TitleStructure of Ku80 von Willebrand domain complexed with APLF Ku Binding Motif
Components
  • GLU-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 / PNK, FHA domain / FHA domain / Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Ku80 / Ku70/Ku80 C-terminal arm ...Aprataxin and PNK-like factor, PBZ domain / Aprataxin and PNK-like factor / PBZ domain / PNK, FHA domain / FHA domain / 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
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 / MOLECULAR REPLACEMENT / Resolution: 1.51076626452 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: GLU-ARG-LYS-ARG-ILE-LEU-PRO-THR-TRP-MET-LEU-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2784
Polymers28,1542
Non-polymers1242
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint3 kcal/mol
Surface area10270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.807, 71.189, 79.527
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 26185.980 Da / Num. of mol.: 1 / Fragment: Ku80 von Willebrand domain / Mutation: C190S, deletion loop (E171 through R188)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: xrcc5, xrcc5-A-prov / 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 GLU-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
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.07 Å3/Da / Density % sol: 40.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5, 20% (w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.51→50 Å / Num. obs: 39709 / % possible obs: 99.8 % / Redundancy: 5.9 % / Biso Wilson estimate: 19.5937445818 Å2 / Rrim(I) all: 0.049 / Net I/σ(I): 50
Reflection shellResolution: 1.51→1.54 Å / Num. unique obs: 1922 / Rrim(I) all: 0.54

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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: 6TYV

6tyv


Resolution: 1.51076626452→29.4430202657 Å / SU ML: 0.129507328798 / Cross valid method: THROUGHOUT / σ(F): 1.47599729749 / Phase error: 23.0203441183
RfactorNum. reflection% reflection
Rfree0.202557392373 1980 5.00037881658 %
Rwork0.177990078727 --
obs0.179194856937 39597 99.6577152493 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.4861613002 Å2
Refinement stepCycle: LAST / Resolution: 1.51076626452→29.4430202657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1679 0 8 172 1859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006774326007931748
X-RAY DIFFRACTIONf_angle_d0.8319317871422365
X-RAY DIFFRACTIONf_chiral_restr0.0510319635665282
X-RAY DIFFRACTIONf_plane_restr0.00548071764131302
X-RAY DIFFRACTIONf_dihedral_angle_d13.3857445307635
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5108-1.54850.2873234029311380.2701941937292611X-RAY DIFFRACTION98.2487491065
1.5485-1.59040.2934809824231360.2413671307112641X-RAY DIFFRACTION99.6054519369
1.5904-1.63720.2560137304381380.2200567595672657X-RAY DIFFRACTION99.8214285714
1.6372-1.690.2369446216421400.2103738169242654X-RAY DIFFRACTION99.6078431373
1.69-1.75040.258722039331380.2046004984422650X-RAY DIFFRACTION99.7495527728
1.7504-1.82050.2194955200351470.2044615228632662X-RAY DIFFRACTION99.5040736805
1.8205-1.90340.2523500289281380.2060772153862648X-RAY DIFFRACTION99.6067214873
1.9034-2.00370.206399511721390.1777908871332654X-RAY DIFFRACTION99.5367070563
2.0037-2.12920.1886001524211420.1647301251262673X-RAY DIFFRACTION99.6107572541
2.1292-2.29350.1939005976531390.1640345055832710X-RAY DIFFRACTION100
2.2935-2.52420.2268867107121450.1713625790672701X-RAY DIFFRACTION100
2.5242-2.88920.1935282643921440.1765570494442723X-RAY DIFFRACTION99.9651324965
2.8892-3.6390.1919019348251440.1748059402352766X-RAY DIFFRACTION100
3.639-29.4430.1796876569111520.164729115622867X-RAY DIFFRACTION99.9007279947
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)
10.5911450473270.199141530845-0.2927709794680.08197561647440.007833372890681.01261861061-0.09319967396640.01735181567880.0358701282273-0.2645353603460.0630850071168-0.0123610625709-0.0936338501428-0.0526143962875-0.0471764866050.184722363960.01277809373710.02788427437620.156289115085-0.004872854926160.1587791540993.31439665476.7495264286213.1921682254
20.8727992595350.49212316904-0.339960462441.531374837250.8103644904661.65086516002-0.1294611926230.209498470443-0.0475834518149-0.45460984742-0.06382860968560.03705351768220.0144754617038-0.175847051111-0.3058746019480.289450190403-0.002197765776920.07887109954610.2000703409710.01910910944020.1952816560168.073982010291.975200690235.68435703883
31.132132656970.8918776163430.3986608867942.45714309261-1.012525280921.13553473534-0.1207865183620.094092533064-0.102826105886-0.374552739596-0.01774954056090.1815627723940.291780455871-0.162450878550.03577511277960.202051349907-0.004120631170870.012773319370.114633432572-0.007183546022350.136946886296-0.35026554103-5.5132443837717.52896915
41.761766609790.406800540564-0.3939969632294.61850809284-2.753549559561.65514361098-0.3205832915650.732997518426-0.0780261893779-1.164264984770.344613674320.397759580660.992616145421-0.668418899995-0.3210825430760.4359065949-0.1288777811060.01610433791840.4197574038490.02627067443890.2302702154022.97633393112-7.35363717695.38746007061
51.384209867630.938624400223-0.4963812235372.1181425013-0.8997358840081.66432275721-0.0998600392932-0.0542890871686-0.029465308622-0.168473149274-0.00697081785892-0.26085682720.1941933627630.0314680491035-0.04684931565430.1603099251390.0075992122510.0267745559570.150759801743-0.0103612770560.1636831953275.52557138894-5.4193209804120.8371995839
60.2183873990570.3218791265790.254025372361.31076489150.275420427791.767069727260.0105288730939-0.01614934335130.03487577663810.167992427450.0124896179817-0.4127905301180.1035086053590.1652247227720.0002980008066870.1614374294840.0162597171626-0.03777204435060.194515364540.01138434068580.2286782476738.015131143591.3361119566327.8428085473
70.576904233579-0.4273683929490.4953857656294.908856091762.906546263392.75897521152-0.06329749031080.304990644595-0.000182154801331-0.1322688530120.351823242182-1.13134670358-0.09473259544840.6408351810460.3276724214140.2412258475480.0134516308847-0.03062267096970.285209808195-0.0190608924120.3737272394029.8255605965719.668319244320.0221244506
81.368435523560.8935028713020.9967652994472.74239947163-0.6906528515481.55531289636-0.07738099628240.159488820136-0.1793596353240.08032093498-0.0500082043788-0.602404544028-0.1701569760380.359485485160.00630380612260.228744791733-0.0128798067732-0.05665900901440.2859936512710.03645003779730.34998782349713.68830370048.375056934223.1449726198
90.5724994804990.276304760709-0.1657854943210.342941686085-0.2633436977840.6649359277850.267171189404-0.1379158216010.2403726695570.136279310973-0.05491329929180.051331687653-0.234133838067-0.2004081606880.02482868255420.259235905998-0.03026132536850.04315551373270.217700043549-0.02214577921940.202021535998-2.2549999905-2.2629639020934.7806205722
100.106198172766-0.0523522534514-0.06873997419060.2352258856020.04906932895490.1450386158770.0474353657086-0.277066434016-0.1989509442230.800582181341-0.0284413873641-0.4803192164060.3781866814770.1128850790320.002916739630710.303748458698-0.0186168603704-0.04951871316460.198944970760.02946277128590.203759156824.91972257263-12.512813094633.8453155212
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 46 )
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 80 )
4X-RAY DIFFRACTION4chain 'A' and (resid 81 through 96 )
5X-RAY DIFFRACTION5chain 'A' and (resid 97 through 134 )
6X-RAY DIFFRACTION6chain 'A' and (resid 135 through 164 )
7X-RAY DIFFRACTION7chain 'A' and (resid 165 through 197 )
8X-RAY DIFFRACTION8chain 'A' and (resid 198 through 235 )
9X-RAY DIFFRACTION9chain 'B' and (resid 181 through 187 )
10X-RAY DIFFRACTION10chain 'B' and (resid 188 through 192 )

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