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- PDB-1q2z: The 3D solution structure of the C-terminal region of Ku86 -

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Basic information

Entry
Database: PDB / ID: 1q2z
TitleThe 3D solution structure of the C-terminal region of Ku86
ComponentsATP-dependent DNA helicase II, 80 kDa subunit
KeywordsPROTEIN BINDING / Ku / DNA repair / protein structure / NMR spectroscopy / DNA-PK / Ku86 / Ku80
Function / homology
Function and homology information


Ku70:Ku80 complex / negative regulation of t-circle formation / DNA end binding / small-subunit processome assembly / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / cellular response to X-ray / nonhomologous end joining complex / regulation of smooth muscle cell proliferation / nuclear telomere cap complex ...Ku70:Ku80 complex / negative regulation of t-circle formation / DNA end binding / small-subunit processome assembly / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / cellular response to X-ray / nonhomologous end joining complex / regulation of smooth muscle cell proliferation / nuclear telomere cap complex / Cytosolic sensors of pathogen-associated DNA / IRF3-mediated induction of type I IFN / recombinational repair / regulation of telomere maintenance / U3 snoRNA binding / positive regulation of neurogenesis / cellular response to fatty acid / hematopoietic stem cell proliferation / protein localization to chromosome, telomeric region / cellular hyperosmotic salinity response / telomeric DNA binding / positive regulation of catalytic activity / 2-LTR circle formation / site of DNA damage / hematopoietic stem cell differentiation / positive regulation of protein kinase activity / ATP-dependent activity, acting on DNA / DNA helicase activity / : / enzyme activator activity / positive regulation of telomere maintenance via telomerase / activation of innate immune response / telomere maintenance / neurogenesis / cellular response to leukemia inhibitory factor / protein-DNA complex / small-subunit processome / Nonhomologous End-Joining (NHEJ) / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cellular response to gamma radiation / double-strand break repair via nonhomologous end joining / double-strand break repair / double-stranded DNA binding / secretory granule lumen / DNA recombination / chromosome, telomeric region / damaged DNA binding / transcription cis-regulatory region binding / ribonucleoprotein complex / response to xenobiotic stimulus / innate immune response / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / DNA damage response / Neutrophil degranulation / protein-containing complex binding / nucleolus / ATP hydrolysis activity / protein-containing complex / DNA binding / RNA binding / extracellular region / nucleoplasm / ATP binding / membrane / nucleus / plasma membrane / cytosol
Similarity search - Function
Ku, C-terminal 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 ...Ku, C-terminal 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 / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
X-ray repair cross-complementing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsHarris, R. / Esposito, D. / Sankar, A. / Maman, J.D. / Hinks, J.A. / Pearl, L.H. / Driscoll, P.C.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: The 3D Solution Structure of the C-terminal Region of Ku86 (Ku86CTR)
Authors: Harris, R. / Esposito, D. / Sankar, A. / Maman, J.D. / Hinks, J.A. / Pearl, L.H. / Driscoll, P.C.
History
DepositionJul 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent DNA helicase II, 80 kDa subunit


Theoretical massNumber of molelcules
Total (without water)13,8681
Polymers13,8681
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein ATP-dependent DNA helicase II, 80 kDa subunit / Lupus Ku autoantigen protein p86 / Ku86 / Ku80 / 86 kDa subunit of Ku antigen / Thyroid- lupus ...Lupus Ku autoantigen protein p86 / Ku86 / Ku80 / 86 kDa subunit of Ku antigen / Thyroid- lupus autoantigen / TLAA / CTC box binding factor 85 kDa subunit / CTCBF / CTC85 / Nuclear factor IV / DNA-repair protein XRCC5


Mass: 13867.651 Da / Num. of mol.: 1 / Fragment: Ku86CTR (591-709)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC5 / Plasmid: pRSET-B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star / References: UniProt: P13010

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
233IPAP
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM U-15N; 20mM Phosphate; 100mM NaCl; 1mM NaN390% H2O/10% D2O
21mM U-13C,15N; 20mM Phosphate; 100mM NaCl; 1mM NaN390% H2O/10% D2O
31mM U-15N; 20mM Phosphate; 100mM NaCl; 1mM NaN3; 5% n-octyl-penta(ethylene glycol):octanol 0.96:190% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 mM NaCl 7.0 ambient 298 K
2100 mM NaCl 7.0 ambient 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
ANSIG1.0.3Kraulis, P.J.data analysis
NMRPipe1Delaglio, F.processing
CNS1.1Brunger, A.T.refinement
VNMR6.1Bvariancollection
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 1959 restraints, 1863 are NOE-derived distance constraints, 174 dihedral angle restraints,96 distance restraints from hydrogen bonds, 96 residual dipolar couplings
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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