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- PDB-6tyv: Structure of Ku80 von Willebrand domain complexed with WRN Ku Bin... -

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Basic information

Entry
Database: PDB / ID: 6tyv
TitleStructure of Ku80 von Willebrand domain complexed with WRN Ku Binding Motif
Components
  • THR-THR-ALA-GLN-GLN-ARG-LYS-CYS-PRO-GLU-TRP-MET-ASN
  • 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


3'-flap-structured DNA binding / positive regulation of strand invasion / telomeric G-quadruplex DNA binding / forked DNA-dependent helicase activity / positive regulation of hydrolase activity / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / regulation of growth rate / telomere maintenance via semi-conservative replication / Ku70:Ku80 complex ...3'-flap-structured DNA binding / positive regulation of strand invasion / telomeric G-quadruplex DNA binding / forked DNA-dependent helicase activity / positive regulation of hydrolase activity / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / regulation of growth rate / telomere maintenance via semi-conservative replication / Ku70:Ku80 complex / t-circle formation / G-quadruplex DNA unwinding / telomeric D-loop disassembly / Y-form DNA binding / four-way junction helicase activity / G-quadruplex DNA binding / MutLalpha complex binding / bubble DNA binding / Processive synthesis on the C-strand of the telomere / Impaired BRCA2 binding to PALB2 / Removal of the Flap Intermediate from the C-strand / protein localization to nucleolus / DNA 3'-5' helicase / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / exonuclease activity / response to UV-C / Resolution of D-loop Structures through Holliday Junction Intermediates / DNA duplex unwinding / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / DNA metabolic process / DNA synthesis involved in DNA repair / telomeric DNA binding / replication fork processing / DNA unwinding involved in DNA replication / 3'-5' DNA helicase activity / Presynaptic phase of homologous DNA pairing and strand exchange / replicative senescence / SUMOylation of DNA damage response and repair proteins / four-way junction DNA binding / DNA helicase activity / isomerase activity / 3'-5' exonuclease activity / cellular response to starvation / telomere maintenance / replication fork / determination of adult lifespan / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / double-strand break repair via homologous recombination / base-excision repair / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / cellular response to gamma radiation / double-strand break repair via nonhomologous end joining / cellular senescence / double-strand break repair / chromosome / manganese ion binding / Processing of DNA double-strand break ends / DNA recombination / DNA replication / Regulation of TP53 Activity through Phosphorylation / response to oxidative stress / chromosome, telomeric region / damaged DNA binding / Hydrolases; Acting on ester bonds / hydrolase activity / nuclear speck / centrosome / DNA damage response / chromatin binding / protein-containing complex binding / nucleolus / magnesium ion binding / protein homodimerization activity / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
Helicase Helix-turn-helix domain / Helix-turn-helix domain / RQC domain / RQC / RQC domain / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / Ku, C-terminal / Ku, C-terminal domain superfamily ...Helicase Helix-turn-helix domain / Helix-turn-helix domain / RQC domain / RQC / RQC domain / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / 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 / Helicase and RNase D C-terminal / Ku70/Ku80 beta-barrel domain / HRDC domain / HRDC domain / HRDC domain profile. / SPOC-like, C-terminal domain superfamily / HRDC domain superfamily / 3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / HRDC-like superfamily / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / von Willebrand factor A-like domain superfamily / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
X-ray repair cross-complementing protein 5 / Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.92611100742 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: THR-THR-ALA-GLN-GLN-ARG-LYS-CYS-PRO-GLU-TRP-MET-ASN


Theoretical massNumber of molelcules
Total (without water)28,1222
Polymers28,1222
Non-polymers00
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-6 kcal/mol
Surface area10420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.112, 71.351, 79.606
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 THR-THR-ALA-GLN-GLN-ARG-LYS-CYS-PRO-GLU-TRP-MET-ASN


Mass: 1936.174 Da / Num. of mol.: 1 / Fragment: WRN Ku Binding Motif / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q14191*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.09 Å3/Da / Density % sol: 41.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Na-HEPES pH 7.5, 25 % (w/v) PEG3000

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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: 1.92→50 Å / Num. obs: 18919 / % possible obs: 99.5 % / Redundancy: 5 % / Biso Wilson estimate: 26.5571151486 Å2 / Rrim(I) all: 0.07 / Net I/σ(I): 34.3
Reflection shellResolution: 1.92→1.95 Å / Num. unique obs: 914 / Rrim(I) all: 0.496

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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: 1JEQ

1jeq


Resolution: 1.92611100742→37.5204611784 Å / SU ML: 0.192610475458 / Cross valid method: FREE R-VALUE / σ(F): 1.3356965295 / Phase error: 25.5808842652
RfactorNum. reflection% reflection
Rfree0.234844595656 944 5.01247809696 %
Rwork0.192609532857 --
obs0.194656196721 18833 95.910572418 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 46.2047717462 Å2
Refinement stepCycle: LAST / Resolution: 1.92611100742→37.5204611784 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1655 0 0 113 1768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007978073890011726
X-RAY DIFFRACTIONf_angle_d0.8650856424722343
X-RAY DIFFRACTIONf_chiral_restr0.0502446886601279
X-RAY DIFFRACTIONf_plane_restr0.00498393311233301
X-RAY DIFFRACTIONf_dihedral_angle_d13.4588767944623
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9262-2.02770.2519015676831020.2262178545641950X-RAY DIFFRACTION74.7813411079
2.0277-2.15470.2884093670181370.221560041652596X-RAY DIFFRACTION99.4541484716
2.1547-2.3210.2586843321951390.2056876329042643X-RAY DIFFRACTION99.7847919656
2.321-2.55450.2575188820211380.2098522909182618X-RAY DIFFRACTION99.6745027125
2.5545-2.92410.2427582548311400.212314447832638X-RAY DIFFRACTION99.5698924731
2.9241-3.68350.2301493691171420.1987222803332673X-RAY DIFFRACTION99.1895701198
3.6835-37.520.2130953457691460.1667821869572771X-RAY DIFFRACTION98.4807562458
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)
14.4207726121-3.632145820360.001063931419433.25118656378-0.8239346480792.463223647550.0254432403148-0.0295396877578-0.00137761915227-0.48937734149-0.0483693434075-0.0377828543451-0.008219077987650.01611597234940.1033870863550.2645585463470.0001680753290540.0006576904846790.23581255138-0.02369589865250.25304384284290.7226281859150.49491560192.2556369586
21.01522365577-0.927342038499-0.7850285663792.756324146411.58796282521.28096701155-0.2173600563380.1655535287280.05825516987-0.8065419520360.00289133434276-0.7780229068530.3198664563750.276621316154-0.2244068858350.4008728277950.02688835400830.1308134453650.2598238919210.02719877618420.28030038090996.1492572888141.61723926486.9005368616
32.84823499952-0.5393482303091.074998836485.725046034060.8464028711531.38635423114-0.264880882473-0.0958529576049-0.134831616694-0.5882160602780.2319410364680.7614635162060.0585441252519-0.4176259304550.3203465561330.190502465135-0.0318173077415-0.01791569797140.2290777012180.01451800311170.26702166387682.4775994602137.919735116100.080598839
41.836766954930.9259373259230.233979668991.56225224313-1.372125772222.05732045944-0.5059893918160.70965170208-0.189088382905-0.6638229947420.341965534106-0.1105606254730.40561812719-0.4058679457580.03266322206680.56142327296-0.1514232867980.02793033279270.4787989625780.01500819109560.19290774530590.695994592135.34469218684.4090043232
52.44804490886-1.83941943658-1.888291389453.167811581170.299677913734.965240413540.0592173343215-0.1169363737390.2622911398350.05850414506590.2643993617550.4737324076360.239658438828-0.1187151404650.4588673770210.184463278564-0.0689007970154-0.07808627606350.1183054005650.06500050600750.36868917806182.0022975082147.47439809295.5666369678
66.79841981095-2.92750926998-2.605210558764.135272656133.624559038447.3501410565-0.162139205725-0.122743815703-0.01462965698920.270101743829-0.0120889124666-0.3954068935710.1905313849350.04761019536910.1888506535540.158420223160.00676849640348-0.01836607365930.1883708476560.009840682096560.15914527031792.6713645194135.739042607103.673569167
71.001623943-0.0205161838569-0.4626421424251.209561489980.04360317182151.38834795858-0.267546788073-0.103528988038-0.338302417660.283691267989-0.0609915187999-0.4623811643020.3442841346080.1844044947250.1530400487910.2081565066780.03449886207330.0494524296460.2492742444740.02126659269270.35546656983196.1920628013140.708355074102.244482369
80.2064117268420.1711838171040.5888408101622.87519176081-0.8974459869222.35372094930.067436528855-0.075618714835-0.01619382005630.0692356449066-0.116623475152-0.5208441194320.006138800390640.3202792225390.1081724630120.1374981767490.0166946064776-0.05433521603490.2819707711450.02028837030230.35143319116499.9218696918147.271412981104.378184411
94.12419266604-3.621980789582.505695158883.75118507453-3.095765715982.94167877085-0.00759407367692-0.399182274889-0.2683768083910.829981599776-0.0968713976892-0.526337018398-0.3052599463150.1096173810590.00933695749360.378894878456-0.0497895327199-0.1779318053140.3327591440330.04554591045450.42180824762599.3779224878152.742538025108.645573973
107.13281262481-1.010868816377.346513830643.61154079617-0.733113363127.59263097923-0.1277727541330.175759557583-0.583854752218-0.257521030734-0.238867001232-0.6456882040980.2274088057850.8596238670820.1860269391630.188160571891-0.02247609358520.0741519944760.4834938389460.1086472881770.528167303987105.699843928149.4496390995.1373415474
116.68481206733-1.70807550067-2.990778036574.88403849954-1.674875252893.22980786649-0.0395609888494-0.2841782098840.3945655208431.83457932907-0.1467780999650.034052455478-0.1699372364780.02440031350.1590689462430.509109803313-0.0766718631072-0.03776310673070.33925541416-0.01089861422010.33866802331689.4613799762137.793519364113.751514052
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 58 )
3X-RAY DIFFRACTION3chain 'A' and (resid 59 through 80 )
4X-RAY DIFFRACTION4chain 'A' and (resid 81 through 95 )
5X-RAY DIFFRACTION5chain 'A' and (resid 96 through 105 )
6X-RAY DIFFRACTION6chain 'A' and (resid 106 through 120 )
7X-RAY DIFFRACTION7chain 'A' and (resid 121 through 145 )
8X-RAY DIFFRACTION8chain 'A' and (resid 146 through 197 )
9X-RAY DIFFRACTION9chain 'A' and (resid 198 through 215 )
10X-RAY DIFFRACTION10chain 'A' and (resid 216 through 235 )
11X-RAY DIFFRACTION11chain 'B' and (resid 8 through 20 )

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