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- PDB-1jjr: The Three-Dimensional Structure of the C-terminal DNA Binding Dom... -

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Basic information

Entry
Database: PDB / ID: 1jjr
TitleThe Three-Dimensional Structure of the C-terminal DNA Binding Domain of Human Ku70
ComponentsTHYROID AUTOANTIGEN
KeywordsDNA BINDING PROTEIN / DNA repair protein / Protein-DNA interaction / Ku70 / solution structure
Function / homology
Function and homology information


Ku70:Ku80 complex / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / cellular response to X-ray / nonhomologous end joining complex / DNA ligation / regulation of smooth muscle cell proliferation / nuclear telomere cap complex / Cytosolic sensors of pathogen-associated DNA ...Ku70:Ku80 complex / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / cellular response to X-ray / nonhomologous end joining complex / DNA ligation / regulation of smooth muscle cell proliferation / nuclear telomere cap complex / Cytosolic sensors of pathogen-associated DNA / double-strand break repair via classical nonhomologous end joining / IRF3-mediated induction of type I IFN / recombinational repair / cellular hyperosmotic salinity response / telomeric DNA binding / 2-LTR circle formation / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / positive regulation of protein kinase activity / ATP-dependent activity, acting on DNA / DNA helicase activity / activation of innate immune response / telomere maintenance / cyclin binding / protein-DNA complex / 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 / scaffold protein binding / double-stranded DNA binding / secretory granule lumen / ficolin-1-rich granule lumen / transcription regulator complex / chromosome, telomeric region / damaged DNA binding / transcription cis-regulatory region binding / innate immune response / negative regulation of DNA-templated transcription / Neutrophil degranulation / protein-containing complex binding / nucleolus / positive regulation of DNA-templated transcription / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular region / nucleoplasm / ATP binding / membrane / nucleus / cytosol
Similarity search - Function
SAP domain / Ku70, bridge and pillars domain superfamily / : / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / Ku70 / 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 ...SAP domain / Ku70, bridge and pillars domain superfamily / : / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / Ku70 / 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 / SAP domain superfamily / SAP domain / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / von Willebrand factor A-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / X-ray repair cross-complementing protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsZhang, Z. / Chen, Y.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: The three-dimensional structure of the C-terminal DNA-binding domain of human Ku70.
Authors: Zhang, Z. / Zhu, L. / Lin, D. / Chen, F. / Chen, D.J. / Chen, Y.
History
DepositionJul 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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: THYROID AUTOANTIGEN


Theoretical massNumber of molelcules
Total (without water)16,9701
Polymers16,9701
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 THYROID AUTOANTIGEN / Ku70


Mass: 16969.523 Da / Num. of mol.: 1 / Fragment: C-terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Ku70 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 339667, UniProt: P12956*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 13C-separated NOESY
1233D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM Ku70_CTD 15N,13C: 100mM Phosphate buffer pH6.090% H2O/10% D2O
21.0 mM Ku70_CTD 15N,13C; 100mM Phosphate buffer pH6.0100% D2O
30.8 mM Ku70_CTD 15N; 100mM Phosphate buffer pH6.090% H2O/10% D2O
Sample conditionsIonic strength: 100 mM Na phosphate / pH: 6 / Pressure: 1 atm / Temperature: 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 spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felix98MSIprocessing
VNMR6.1BVariancollection
DYANA1.5Peter Gntert, Christian Mumenthaler & Torsten Herrmannstructure solution
X-PLORCNS 1.0A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros, R.W.Grosse-Kunstleve,structure solution
X-PLORCNS 1.0A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros, R.W.Grosse-Kunstleve,refinement
RefinementMethod: simulated annealing / Software ordinal: 1
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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