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- PDB-1ewi: HUMAN REPLICATION PROTEIN A: GLOBAL FOLD OF THE N-TERMINAL RPA-70... -

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Basic information

Entry
Database: PDB / ID: 1ewi
TitleHUMAN REPLICATION PROTEIN A: GLOBAL FOLD OF THE N-TERMINAL RPA-70 DOMAIN REVEALS A BASIC CLEFT AND FLEXIBLE C-TERMINAL LINKER
ComponentsREPLICATION PROTEIN ADNA replication
KeywordsREPLICATION / 5-stranded anti-parallel / beta barrel
Function / homology
Function and homology information


protein localization to chromosome / DNA replication factor A complex / chromatin-protein adaptor activity / protein localization to site of double-strand break / single-stranded telomeric DNA binding / Removal of the Flap Intermediate / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding ...protein localization to chromosome / DNA replication factor A complex / chromatin-protein adaptor activity / protein localization to site of double-strand break / single-stranded telomeric DNA binding / Removal of the Flap Intermediate / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / site of DNA damage / Presynaptic phase of homologous DNA pairing and strand exchange / telomere maintenance via telomerase / Activation of the pre-replicative complex / PCNA-Dependent Long Patch Base Excision Repair / Regulation of HSF1-mediated heat shock response / HSF1 activation / mismatch repair / Activation of ATR in response to replication stress / SUMOylation of DNA damage response and repair proteins / telomere maintenance / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / meiotic cell cycle / nucleotide-excision repair / Fanconi Anemia Pathway / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / double-strand break repair via homologous recombination / Translesion Synthesis by POLH / base-excision repair / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / Dual Incision in GG-NER / DNA-templated DNA replication / PML body / Meiotic recombination / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / site of double-strand break / single-stranded DNA binding / Processing of DNA double-strand break ends / DNA recombination / Regulation of TP53 Activity through Phosphorylation / DNA replication / damaged DNA binding / chromosome, telomeric region / DNA repair / DNA damage response / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Replication factor-A protein 1, N-terminal domain / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / Replication factor A, C-terminal / Replication factor-A C terminal domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain ...Replication factor-A protein 1, N-terminal domain / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / Replication factor A, C-terminal / Replication factor-A C terminal domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Replication protein A 70 kDa DNA-binding subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsJacobs, D.M. / Lipton, A.S. / Isern, N.G. / Daughdrill, G.W. / Lowry, D.F. / Gomes, X. / Wold, M.S.
CitationJournal: J.Biomol.NMR / Year: 1999
Title: Human replication protein A: global fold of the N-terminal RPA-70 domain reveals a basic cleft and flexible C-terminal linker.
Authors: Jacobs, D.M. / Lipton, A.S. / Isern, N.G. / Daughdrill, G.W. / Lowry, D.F. / Gomes, X. / Wold, M.S.
History
DepositionApr 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 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: REPLICATION PROTEIN A


Theoretical massNumber of molelcules
Total (without water)12,4881
Polymers12,4881
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)1 / 8structures with the least restraint violations
Representativefewest violations

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Components

#1: Protein REPLICATION PROTEIN A / DNA replication / RPA70


Mass: 12487.619 Da / Num. of mol.: 1 / Fragment: N-TERMINAL FRAGMENT (RESIDUES 1-114) / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P27694

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
121HN(CA)CB
131CBCACONNH
NMR detailsText: Due to aggregation during aging, NMR spectra were recorded with freshly prepared samples.

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Sample preparation

DetailsContents: 1mM d169, 100 mM Tris, 100 mM Tris-HCL, 0.25 mM EDTA, 50 mM NaCl, 0.2% NaN3 and 1mM DTT, pH 7.6
Solvent system: 90% H20, 10% D20
Sample conditionsIonic strength: 50 mM / pH: 7.6 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
Felix97msidata analysis
X-PLOR3Brungerstructure solution
X-PLOR3Brungerrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 8 / Conformers submitted total number: 1

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