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- PDB-2jpd: Solution structure of the ERCC1 central domain -

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Basic information

Entry
Database: PDB / ID: 2jpd
TitleSolution structure of the ERCC1 central domain
ComponentsDNA excision repair protein ERCC-1
KeywordsDNA BINDING PROTEIN / PROTEIN
Function / homology
Function and homology information


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 complex / t-circle formation ...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 complex / t-circle formation / response to sucrose / UV protection / mitotic recombination / post-embryonic hemopoiesis / isotype switching / UV-damage excision repair / HDR through Single Strand Annealing (SSA) / oogenesis / TFIID-class transcription factor complex binding / response to X-ray / response to immobilization stress / replicative senescence / 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 / promoter-specific chromatin binding / nucleotide-excision repair / Fanconi Anemia Pathway / multicellular organism growth / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / double-strand break repair via nonhomologous end joining / male gonad development / single-stranded DNA binding / spermatogenesis / response to oxidative stress / cell population proliferation / damaged DNA binding / chromosome, telomeric region / DNA repair / nucleoplasm / cytoplasm
Similarity search - Function
ERCC1/RAD10/SWI10 family / : / Binding domain of DNA repair protein Ercc1 (rad10/Swi10) / Rossmann fold - #10130 / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsTripsianes, K. / Folkers, G. / Zheng, C. / Das, D. / Grinstead, J.S. / Kaptein, R. / Boelens, R.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: Analysis of the XPA and ssDNA-binding surfaces on the central domain of human ERCC1 reveals evidence for subfunctionalization
Authors: Tripsianes, K. / Folkers, G.E. / Zheng, C. / Das, D. / Grinstead, J.S. / Kaptein, R. / Boelens, R.
History
DepositionMay 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents ..._pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Revision 1.5May 8, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA excision repair protein ERCC-1


Theoretical massNumber of molelcules
Total (without water)15,4621
Polymers15,4621
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
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: 15461.830 Da / Num. of mol.: 1 / Fragment: residues 96-219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC1 / Production host: Escherichia coli (E. coli) / References: UniProt: P07992

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1213D 1H-15N NOESY
1313D 1H-13C NOESY
1413D (H)CCH 1H-13C NOESY
1512D NOESY 15N filtered

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Sample preparation

DetailsContents: 50 mM sodium phosphate, 100 mM sodium chloride, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
50 mMsodium phosphate1
100 mMsodium chloride1
Sample conditionsIonic strength: 0.2 / pH: 5.5 / Pressure: ambient / Temperature: 290 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
SparkyGoddardpeak picking
TALOSCornilescu, Delaglio and Baxgeometry optimization
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / 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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