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- PDB-2mut: Solution structure of the F231L mutant ERCC1-XPF dimerization region -

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Basic information

Entry
Database: PDB / ID: 2mut
TitleSolution structure of the F231L mutant ERCC1-XPF dimerization region
Components
  • DNA excision repair protein ERCC-1
  • DNA repair endonuclease XPF
KeywordsHYDROLASE / ERCC1-XPF / F231L / Nucleotide Excision Repair
Function / homology
Function and homology information


negative regulation of double-stranded telomeric DNA binding / positive regulation of t-circle formation / pyrimidine dimer repair by nucleotide-excision repair / syncytium formation / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / negative regulation of telomere maintenance / nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair factor 1 complex ...negative regulation of double-stranded telomeric DNA binding / positive regulation of t-circle formation / pyrimidine dimer repair by nucleotide-excision repair / syncytium formation / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / negative regulation of telomere maintenance / nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair factor 1 complex / nucleotide-excision repair complex / response to sucrose / t-circle formation / single-stranded DNA endodeoxyribonuclease activity / resolution of meiotic recombination intermediates / mitotic recombination / UV protection / post-embryonic hemopoiesis / isotype switching / 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 / response to cadmium ion / interstrand cross-link repair / response to UV / telomere maintenance / response to nutrient / DNA endonuclease activity / insulin-like growth factor receptor signaling pathway / regulation of autophagy / promoter-specific chromatin binding / determination of adult lifespan / 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 / damaged DNA binding / chromosome, telomeric region / 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 / restrained molecular dynamics
Model detailslowest energy, model1
AuthorsFaridounnia, M. / Wienk, H. / Kovacic, L. / Folkers, G.E. / Jaspers, N.G.J. / Kaptein, R. / Hoeijmakers, J.H.J. / Boelens, R.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: The Cerebro-oculo-facio-skeletal Syndrome Point Mutation F231L in the ERCC1 DNA Repair Protein Causes Dissociation of the ERCC1-XPF Complex.
Authors: Faridounnia, M. / Wienk, H. / Kovacic, L. / Folkers, G.E. / Jaspers, N.G. / Kaptein, R. / Hoeijmakers, J.H. / Boelens, R.
History
DepositionSep 17, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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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)20,2162
Polymers20,2162
Non-polymers00
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 DNA excision repair protein ERCC-1


Mass: 10985.669 Da / Num. of mol.: 1 / Fragment: UNP residues 220-297 / Mutation: F231L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P07992
#2: 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: 9230.518 Da / Num. of mol.: 1 / Fragment: UNP residues 834-916
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC4, ERCC11, XPF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
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
1112D HSQC
121triple resonance
131NOESY
1412D HSQC
1512D HSQC

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Sample preparation

DetailsContents: 0.4 mM [U-100% 13C; U-100% 15N] protein_1, 0.4 mM [U-100% 13C; U-100% 15N] protein_2, 8 % D2O, 50 mM sodium phosphate, 100 mM sodium chloride, 92% H2O/8% D2O
Solvent system: 92% H2O/8% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMentity_1-1[U-100% 13C; U-100% 15N]1
0.4 mMentity_2-2[U-100% 13C; U-100% 15N]1
8 %D2O-31
50 mMsodium phosphate-41
100 mMsodium chloride-51
Sample conditionsIonic strength: 250 / pH: 7.0 / Pressure: ambient / Temperature: 290 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE7503
Bruker AvanceBrukerAVANCE9004

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CINGDoreleijers et alvalidation
RefinementMethod: restrained molecular dynamics / 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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