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- PDB-1z00: Solution structure of the C-terminal domain of ERCC1 complexed wi... -

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Basic information

Entry
Database: PDB / ID: 1z00
TitleSolution structure of the C-terminal domain of ERCC1 complexed with the C-terminal domain of XPF
Components
  • DNA excision repair protein ERCC-1
  • DNA repair endonuclease XPF
KeywordsHYDROLASE / helix-hairpin-helix
Function / homology
Function and homology information


negative regulation of double-stranded telomeric DNA binding / double-strand break repair via single-strand annealing, removal of nonhomologous ends / positive regulation of t-circle formation / negative regulation of telomere maintenance / pyrimidine dimer repair by nucleotide-excision repair / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / syncytium formation / nucleotide-excision repair factor 1 complex ...negative regulation of double-stranded telomeric DNA binding / double-strand break repair via single-strand annealing, removal of nonhomologous ends / positive regulation of t-circle formation / negative regulation of telomere maintenance / pyrimidine dimer repair by nucleotide-excision repair / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / syncytium formation / nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair complex / t-circle formation / resolution of meiotic recombination intermediates / response to sucrose / single-stranded DNA endodeoxyribonuclease activity / UV protection / post-embryonic hemopoiesis / isotype switching / mitotic recombination / UV-damage excision repair / negative regulation of telomere maintenance via telomere lengthening / HDR through Single Strand Annealing (SSA) / oogenesis / TFIID-class transcription factor complex binding / response to immobilization stress / response to X-ray / replicative senescence / positive regulation of transcription initiation by RNA polymerase II / embryonic organ development / interstrand cross-link repair / response to cadmium ion / response to UV / telomere maintenance / response to nutrient / insulin-like growth factor receptor signaling pathway / DNA endonuclease activity / regulation of autophagy / determination of adult lifespan / promoter-specific chromatin binding / nucleotide-excision repair / Fanconi Anemia Pathway / double-strand break repair via homologous recombination / multicellular organism growth / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / double-strand break repair via nonhomologous end joining / Dual incision in TC-NER / male gonad development / cellular response to UV / single-stranded DNA binding / spermatogenesis / response to oxidative stress / cell population proliferation / chromosome, telomeric region / damaged DNA binding / Hydrolases; Acting on ester bonds / DNA repair / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
DNA repair protein XPF / : / ERCC1/RAD10/SWI10 family / : / Binding domain of DNA repair protein Ercc1 (rad10/Swi10) / ERCC4 domain / ERCC4 domain / ERCC4 domain / Helix-hairpin-helix motif / RuvA domain 2-like ...DNA repair protein XPF / : / ERCC1/RAD10/SWI10 family / : / Binding domain of DNA repair protein Ercc1 (rad10/Swi10) / ERCC4 domain / ERCC4 domain / ERCC4 domain / Helix-hairpin-helix motif / RuvA domain 2-like / Restriction endonuclease type II-like / Helix-hairpin-helix domain / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA excision repair protein ERCC-1 / DNA repair endonuclease XPF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / water refinment in CNS
AuthorsTripsianes, K. / Folkers, G. / Ab, E. / Das, D. / Odijk, H. / Jaspers, N.G.J. / Hoeijmakers, J.H.J. / Kaptein, R. / Boelens, R.
CitationJournal: Structure / Year: 2005
Title: The Structure of the Human ERCC1/XPF Interaction Domains Reveals a Complementary Role for the Two Proteins in Nucleotide Excision Repair
Authors: Tripsianes, K. / Folkers, G. / Ab, E. / Das, D. / Odijk, H. / Jaspers, N.G.J. / Hoeijmakers, J.H.J. / Kaptein, R. / Boelens, R.
History
DepositionMar 1, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 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: DNA excision repair protein ERCC-1
B: DNA repair endonuclease XPF


Theoretical massNumber of molelcules
Total (without water)19,2312
Polymers19,2312
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 DNA excision repair protein ERCC-1


Mass: 10000.475 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(Rosetta) novagen / References: UniProt: P07992
#2: Protein DNA repair endonuclease XPF / DNA excision repair protein ERCC-4 / DNA-repair protein complementing XP-F cell / Xeroderma ...DNA excision repair protein ERCC-4 / DNA-repair protein complementing XP-F cell / Xeroderma pigmentosum group F complementing protein


Mass: 9230.518 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(Rosetta) novagen
References: UniProt: Q92889, Hydrolases; Acting on ester bonds

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D NOESY-(13C,1H)-HSQC
1213D NOESY-(15N,1H)-HSQC
1313D (13C)-HMQC-NOESY-(13C,1H)-HSQC
1413D (13C)-HMQC-NOESY-(15N 1H)-HSQC
1522D NOESY
1622D NOESY 15N FILTERED

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM ERCC1-XPF U-15N,13C; 50mM phosphate buffer NA: 92% H2O, 8% D2O92% H2O, 8% D2O
21mM ERCC1-XPF U-15N; 50mM phosphate buffer NA: 92% H2O, 8% D2O92% H2O, 8% D2O
Sample conditionsIonic strength: 50mM phosphate, 100mM NaCl / pH: 7.0 / Pressure: 1 atm / Temperature: 295.5 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE7001
Bruker AVANCEBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5collection
NMRPipe2.3Delaglioprocessing
Sparky3.11Goddard and Knellerdata analysis
CYANA2Guntertstructure solution
CNS1.1Brungerrefinement
RefinementMethod: water refinment in CNS / Software ordinal: 1
Details: 4547 NOE-derived distance restraints, 197 TALOS based dihedral angle restraints and distance restraints for 52 hydrogen bonds
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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