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- PDB-2jnw: Solution structure of a ERCC1-XPA heterodimer -

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Basic information

Entry
Database: PDB / ID: 2jnw
TitleSolution structure of a ERCC1-XPA heterodimer
Components
  • DNA excision repair protein ERCC-1
  • DNA-repair protein complementing XP-A cells
KeywordsDNA BINDING PROTEIN / ercc1 / xpa / NER / recruitment
Function / homology
Function and homology information


positive regulation of t-circle formation / 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, DNA damage recognition / nucleotide-excision repair complex ...positive regulation of t-circle formation / 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, DNA damage recognition / nucleotide-excision repair complex / t-circle formation / negative regulation of telomere maintenance / response to auditory stimulus / response to sucrose / mitotic recombination / UV protection / post-embryonic hemopoiesis / isotype switching / UV-damage excision repair / HDR through Single Strand Annealing (SSA) / oogenesis / TFIID-class transcription factor complex binding / response to immobilization stress / replicative senescence / protein localization to nucleus / response to X-ray / positive regulation of transcription initiation by RNA polymerase II / embryonic organ development / interstrand cross-link repair / response to cadmium ion / response to nutrient / insulin-like growth factor receptor signaling pathway / determination of adult lifespan / nucleotide-excision repair / Fanconi Anemia Pathway / promoter-specific chromatin binding / base-excision repair / multicellular organism growth / double-strand break repair via nonhomologous end joining / Dual Incision in GG-NER / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / male gonad development / Dual incision in TC-NER / sequence-specific double-stranded DNA binding / single-stranded DNA binding / spermatogenesis / response to oxidative stress / damaged DNA binding / chromosome, telomeric region / cell population proliferation / nuclear body / protein domain specific binding / DNA repair / protein homodimerization activity / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
ERCC1/RAD10/SWI10 family / : / Binding domain of DNA repair protein Ercc1 (rad10/Swi10) / XPA protein N-terminal / Rossmann fold - #10130 / XPA / Zinc finger, XPA-type, conserved site / XPA, C-terminal / XPA, conserved site / XPA protein C-terminus ...ERCC1/RAD10/SWI10 family / : / Binding domain of DNA repair protein Ercc1 (rad10/Swi10) / XPA protein N-terminal / Rossmann fold - #10130 / XPA / Zinc finger, XPA-type, conserved site / XPA, C-terminal / XPA, conserved site / XPA protein C-terminus / XPA protein signature 1. / XPA protein signature 2. / XPA domain superfamily / Putative DNA-binding domain superfamily / RuvA domain 2-like / Restriction endonuclease type II-like / Helix-hairpin-helix domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA excision repair protein ERCC-1 / DNA repair protein complementing XP-A cells
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsStructure of the ERCC1-binding region of XPA bound to the central domain of ERCC1
AuthorsTsodikov, O.V. / Ivanov, D. / Orelli, B. / Staresincic, L. / Scharer, O.D. / Wagner, G.
CitationJournal: Embo J. / Year: 2007
Title: Structural basis for the recruitment of ERCC1-XPF to nucleotide excision repair complexes by XPA
Authors: Tsodikov, O.V. / Ivanov, D. / Orelli, B. / Staresincic, L. / Shoshani, I. / Oberman, R. / Scharer, O.D. / Wagner, G. / Ellenberger, T.
History
DepositionFeb 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 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 1.3Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA excision repair protein ERCC-1
B: DNA-repair protein complementing XP-A cells


Theoretical massNumber of molelcules
Total (without water)16,6392
Polymers16,6392
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein DNA excision repair protein ERCC-1


Mass: 15117.362 Da / Num. of mol.: 1 / Fragment: Central domain, residues 96-214
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07992
#2: Protein/peptide DNA-repair protein complementing XP-A cells / Xeroderma pigmentosum group A-complementing protein


Mass: 1521.688 Da / Num. of mol.: 1 / Fragment: ERCC1-binding region, residues 67-80 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human).
References: UniProt: P23025

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Structure of the ERCC1-binding region of XPA bound to the central domain of ERCC1
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA
121HN(CO)CA
131HN(CA)CB
141HN(COCA)CB
151HNCO
161HN(CA)CO

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Sample preparation

Details
Solution-IDContentsSolvent system
10.25 mM [U-100% 13C; U-100% 15N] ERCC1, 20 mM Tris-HCl pH 7.2, 50 mM NaCl, 2 mM beta-mercaptoethanol, 0.1 mM EDTA, 90% H2O, 10% D2O90% H2O/10% D2O
20.25 mM [U-100% 15N, 100% 2H] ERCC1, 20 mM Tris-HCl pH 7.2, 50 mM NaCl, 2 mM beta-mercaptoethanol, 0.1 mM EDTA, 90% H2O, 10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.25 mMERCC1[U-100% 13C; U-100% 15N]1
0.25 mMERCC1[U-100% 15N, 100% 2H]2
Sample conditionsIonic strength: 0.05 / pH: 7.2 / Pressure: ambient / Temperature: 295 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7502

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Processing

NMR softwareName: X-PLOR NIH / Developer: NIH / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: XPLOR-NIH was used. In the refinement, low-resolution X-ray diffraction data was used as well. ERCC1 structure was taken from the related PDB entry and tight geometrical restraints were ...Details: XPLOR-NIH was used. In the refinement, low-resolution X-ray diffraction data was used as well. ERCC1 structure was taken from the related PDB entry and tight geometrical restraints were imposed on ERCC1 geometry.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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