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- PDB-2kuo: Structure and identification of ADP-ribose recognition motifs of ... -

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Basic information

Entry
Database: PDB / ID: 2kuo
TitleStructure and identification of ADP-ribose recognition motifs of APLF and role in the DNA damage response
ComponentsAprataxin and PNK-like factor
KeywordsMETAL BINDING PROTEIN / aprataxin PNK-like factor (APLF) / poly ADP-ribose (PAR) / PAR-binding zinc finger (PBZ) / DNA damage / ADP-ribose / ADP-ribosylation / DNA repair / Metal-binding / Nucleotide-binding / Nucleus / Zinc / Zinc-finger
Function / homology
Function and homology information


ADP-D-ribose modification-dependent protein binding / regulation of isotype switching / histone chaperone activity / 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 / site of DNA damage / protein folding chaperone ...ADP-D-ribose modification-dependent protein binding / regulation of isotype switching / histone chaperone activity / 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 / site of DNA damage / protein folding chaperone / DNA-(apurinic or apyrimidinic site) endonuclease activity / protein localization to chromatin / 3'-5' exonuclease activity / embryo implantation / DNA endonuclease activity / double-strand break repair via nonhomologous end joining / double-strand break repair / site of double-strand break / histone binding / Hydrolases; Acting on ester bonds / nucleotide binding / DNA repair / DNA damage response / nucleoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
Aprataxin and PNK-like factor, PBZ domain / Aprataxin and PNK-like factor / PBZ domain / PNK, FHA domain / FHA domain / SMAD/FHA domain superfamily
Similarity search - Domain/homology
Aprataxin and PNK-like factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsLi, G.Y. / McCulloch, R.D. / Fenton, A. / Cheung, M. / Meng, L. / Ikura, M. / Koch, C.A.
CitationJournal: To be Published
Title: Structure and identification of ADP-ribose recognition motifs of aprataxin PNK-like factor (APLF) required for the interaction with sites of DNA damage response
Authors: Li, G.Y. / McCulloch, R.D. / Fenton, A. / Cheung, M. / Meng, L. / Ikura, M. / Koch, C.A.
History
DepositionFeb 23, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 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: Aprataxin and PNK-like factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4033
Polymers10,2721
Non-polymers1312
Water0
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 Aprataxin and PNK-like factor / Apurinic-apyrimidinic endonuclease APLF / PNK and APTX-like FHA domain-containing protein / XRCC1- ...Apurinic-apyrimidinic endonuclease APLF / PNK and APTX-like FHA domain-containing protein / XRCC1-interacting protein 1


Mass: 10272.325 Da / Num. of mol.: 1 / Fragment: APLF TZF
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APLF, APLF(C2orf13), C2orf13, PALF, XIP1 / Plasmid: pGEX4T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q8IW19
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1322D 1H-1H NOESY
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D H(CCO)NH
1813D C(CO)NH
1923D (H)CCH-TOCSY
11013D (H)CCH-COSY
11113D 1H-15N NOESY
11223D 1H-13C NOESY
31352D 1H-15N IPAP HSQC
11432D 1H-15N HSQC
21542D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-0.8 mM [U-100% 13C; U-100% 15N] APLF Tandem ZF, 20 mM Bis-tris, 50 mM sodium chloride, 1 mM sodium azide, 0.05 mM zinc chloride, 93% H2O/7% D2O93% H2O/7% D2O
20.5-0.8 mM [U-100% 13C; U-100% 15N] APLF Tandem ZF, 20 mM Bis-tris, 50 mM sodium chloride, 1 mM sodium azide, 0.05 mM zinc chloride, 99% D2O99% D2O
30.1 mM [U-100% 15N] APLF Tandem ZF, 20 mM Bis-tris, 50 mM sodium chloride, 1 mM sodium azide, 0.05 mM zinc chloride, 93% H2O/7% D2O93% H2O/7% D2O
40.1 mM [U-100% 15N] APLF Tandem ZF, 20 mM sodium phosphate, 150 mM potassium chloride, 1 mM sodium azide, 0.05 mM zinc chloride, 2 mM magnesium chloride, 93% H2O/7% D2O93% H2O/7% D2O
50.5 mM [U-100% 15N] APLF Tandem ZF, 20 mM Bis-tris, 500 mM sodium chloride, 1 mM sodium azide, 0.05 mM zinc chloride, 10 mg/mL Pf1 phage, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMAPLF Tandem ZF[U-100% 13C; U-100% 15N]0.5-0.81
20 mMBis-tris1
50 mMsodium chloride1
1 mMsodium azide1
0.05 mMzinc chloride1
mMAPLF Tandem ZF[U-100% 13C; U-100% 15N]0.5-0.82
20 mMBis-tris2
50 mMsodium chloride2
1 mMsodium azide2
0.05 mMzinc chloride2
0.1 mMAPLF Tandem ZF[U-100% 15N]3
20 mMBis-tris3
50 mMsodium chloride3
1 mMsodium azide3
0.05 mMzinc chloride3
0.1 mMAPLF Tandem ZF[U-100% 15N]4
20 mMsodium phosphate4
150 mMpotassium chloride4
1 mMsodium azide4
0.05 mMzinc chloride4
2 mMmagnesium chloride4
0.5 mMAPLF Tandem ZF[U-100% 15N]5
20 mMBis-tris5
500 mMsodium chloride5
1 mMsodium azide5
0.05 mMzinc chloride5
10 mg/mLPf1 phage5
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 6.0 ambient 298 K
2150 7.4 ambient 298 K
3500 6.0 ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, P. et al.structure solution
CNS1.1Brunger, A. et al.refinement
MOLMOL2kKoradi, R. et al.data analysis
NMRPipeDelaglio, F. et al.processing
TALOSCornilescu, G. et al.chemical shift based dihedral angle calculation
TopSpinBruker Biospincollection
XEASYBartels, C. et al.peak picking
XEASYBartels, C. et al.chemical shift assignment
XEASYBartels, C. et al.data analysis
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1 / Details: CYANA, CNS
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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