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- PDB-1rw2: Three-dimensional structure of Ku80 CTD -

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Basic information

Entry
Database: PDB / ID: 1rw2
TitleThree-dimensional structure of Ku80 CTD
ComponentsATP-dependent DNA helicase II, 80 kDa subunit
KeywordsDNA BINDING PROTEIN / Ku80 / NHEJ / DNA-PK
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 / Nonhomologous End-Joining (NHEJ) / small-subunit processome / 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
AuthorsZhang, Z. / Hu, W. / Cano, L. / Lee, T.D. / Chen, D.J. / Chen, Y.
CitationJournal: STRUCTURE / Year: 2004
Title: Solution structure of the C-terminal domain of Ku80 suggests important sites for protein-protein interactions.
Authors: Zhang, Z. / Hu, W. / Cano, L. / Lee, T.D. / Chen, D.J. / Chen, Y.
History
DepositionDec 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2003Provider: 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
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)17,3521
Polymers17,3521
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)10 / 40structures with the least restraint violations,target function
Representative

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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: 17351.535 Da / Num. of mol.: 1 / Fragment: Ku80 C-terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ku80 (566-710) / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P13010

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
121(H)CCH-TOCSY
132HN(CA)CB, C(CO)NH, HNCO, HN(CA)CO, H(CCO)NH, HBHA(CO)NH
1433D 15N-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1Approximately 1 mM N-15/C-13 labeled protein in 100 mM phosphate buffer, pH 6.0, and 5 mM DTT100% D2O
2Approximately 1 mM N-15/C-13 labeled protein in 100 mM phosphate buffer, pH 6.0, and 5 mM DTT90% H2O/10% D2O
3Approximately 1 mM N-15 labeled protein in 100 mM phosphate buffer, pH 6.0, an90% H2O/10% D2O
Sample conditionsIonic strength: 100 mM phosphate buffer / pH: 6.0 / Pressure: 1 atmosphere / Temperature: 298 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
VNMR6.1Variancollection
Felix98, 2000Accelrysprocessing
Felix98, 2000Accelrysdata analysis
DIANA1.5Peter Guntert, Christian Mumenthaler and Torsten Herrmannstructure solution
ARIA1.2Jens Linge, Michael Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 2449 restraints, 2180 are NOE-derived distance constraints, 201 dihedral angle restraints,68 residue dipolar coupling
NMR ensembleConformer selection criteria: structures with the least restraint violations,target function
Conformers calculated total number: 40 / Conformers submitted total number: 10

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