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- PDB-2kn7: Structure of the XPF-single strand DNA complex -

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Basic information

Entry
Database: PDB / ID: 2kn7
TitleStructure of the XPF-single strand DNA complex
Components
  • DNA (5'-D(*CP*AP*GP*TP*GP*GP*CP*TP*GP*A)-3')
  • DNA repair endonuclease XPF
KeywordsHYDROLASE/DNA / NER / XPF/ERCC1 / HhH / Protein-ssDNA complex / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair complex / negative regulation of telomere maintenance / single-stranded DNA endodeoxyribonuclease activity / resolution of meiotic recombination intermediates / UV protection ...telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair complex / negative regulation of telomere maintenance / single-stranded DNA endodeoxyribonuclease activity / resolution of meiotic recombination intermediates / UV protection / negative regulation of telomere maintenance via telomere lengthening / HDR through Single Strand Annealing (SSA) / TFIID-class transcription factor complex binding / response to UV / telomere maintenance / DNA endonuclease activity / nucleotide-excision repair / Fanconi Anemia Pathway / promoter-specific chromatin binding / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / cellular response to UV / single-stranded DNA binding / damaged DNA binding / Hydrolases; Acting on ester bonds / chromosome, telomeric region / regulation of autophagy / DNA repair / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
DNA repair protein XPF / : / ERCC4 domain / ERCC4 domain / ERCC4 domain / RuvA domain 2-like / Restriction endonuclease type II-like / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA repair endonuclease XPF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsDas, D. / Folkers, G.E. / van Dijk, M. / Jaspers, N.G.J. / Hoeijmakers, J.H.J. / Kaptein, R. / Boelens, R.
CitationJournal: Structure / Year: 2012
Title: The structure of the XPF-ssDNA complex underscores the distinct roles of the XPF and ERCC1 helix- hairpin-helix domains in ss/ds DNA recognition
Authors: Das, D. / Folkers, G.E. / van Dijk, M. / Jaspers, N.G.J. / Hoeijmakers, J.H.J. / Kaptein, R. / Boelens, R.
History
DepositionAug 16, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 4, 2012Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA repair endonuclease XPF
D: DNA repair endonuclease XPF
B: DNA (5'-D(*CP*AP*GP*TP*GP*GP*CP*TP*GP*A)-3')
C: DNA (5'-D(*CP*AP*GP*TP*GP*GP*CP*TP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)21,0174
Polymers21,0174
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein DNA repair endonuclease XPF / DNA excision repair protein ERCC-4 / DNA repair protein complementing XP-F cells / Xeroderma ...DNA excision repair protein ERCC-4 / DNA repair protein complementing XP-F cells / Xeroderma pigmentosum group F-complementing protein


Mass: 7423.440 Da / Num. of mol.: 2 / Fragment: residues in UNP 842-908
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XPF / Production host: Escherichia coli (E. coli)
References: UniProt: Q92889, Hydrolases; Acting on ester bonds
#2: DNA chain DNA (5'-D(*CP*AP*GP*TP*GP*GP*CP*TP*GP*A)-3')


Mass: 3085.028 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-13C NOESY
1213D 1H-15N NOESY
1313D CBCA(CO)NH
1412D 1H-15N HSQC
1512D 1H-13C HSQC
1613D (H)CCH-TOCSY
1713D C(CO)NH

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Sample preparation

DetailsContents: 80mM sodium phosphate-1, 2mM sodium chloride-2, 0.005-0.010mM AEBSF protease inhibitor-3, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentConc. range (mg/ml)Solution-ID
80 mMsodium phosphate-11
2 mMsodium chloride-21
mMAEBSF protease inhibitor-30.005-0.0101
Sample conditionsIonic strength: 80-100 / pH: 5.2 / Pressure: ambient / Temperature: 293.8 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Bruker Biospinprocessing
CYANAHerrmann, Guntert and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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