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- PDB-1ynx: Solution structure of DNA binding domain A (DBD-A) of S.cerevisia... -

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Basic information

Entry
Database: PDB / ID: 1ynx
TitleSolution structure of DNA binding domain A (DBD-A) of S.cerevisiae Replication Protein A (RPA)
ComponentsReplication factor-A protein 1
KeywordsDNA BINDING PROTEIN / Canonical OB fold
Function / homology
Function and homology information


heteroduplex formation / sporulation / DNA replication factor A complex / Gap-filling DNA repair synthesis and ligation in GG-NER / telomere maintenance via telomere lengthening / Removal of the Flap Intermediate / mitotic recombination / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI ...heteroduplex formation / sporulation / DNA replication factor A complex / Gap-filling DNA repair synthesis and ligation in GG-NER / telomere maintenance via telomere lengthening / Removal of the Flap Intermediate / mitotic recombination / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Translesion Synthesis by POLH / Activation of the pre-replicative complex / telomere maintenance via recombination / Termination of translesion DNA synthesis / Activation of ATR in response to replication stress / reciprocal meiotic recombination / Gap-filling DNA repair synthesis and ligation in TC-NER / : / DNA topological change / Dual incision in TC-NER / telomere maintenance via telomerase / telomere maintenance / condensed nuclear chromosome / nucleotide-excision repair / establishment of protein localization / double-strand break repair via homologous recombination / single-stranded DNA binding / double-stranded DNA binding / sequence-specific DNA binding / DNA replication / chromosome, telomeric region / protein ubiquitination / DNA repair / mRNA binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
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 ...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 factor A protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / Torsional Angle Dynamics with Internal Variable Module
AuthorsPark, C.J. / Lee, J.H. / Choi, B.S.
CitationJournal: Nucleic Acids Res. / Year: 2005
Title: Solution structure of the DNA-binding domain of RPA from Saccharomyces cerevisiae and its interaction with single-stranded DNA and SV40 T antigen
Authors: Park, C.J. / Lee, J.H. / Choi, B.S.
History
DepositionJan 26, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 10, 2006Provider: 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: Replication factor-A protein 1


Theoretical massNumber of molelcules
Total (without water)13,2661
Polymers13,2661
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)22 / 100structures with the lowest energy
RepresentativeModel #12lowest energy

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Components

#1: Protein Replication factor-A protein 1 / Replication Protein A / RF-A / Single-stranded DNA-binding protein / DNA binding protein BUF2 / ...Replication Protein A / RF-A / Single-stranded DNA-binding protein / DNA binding protein BUF2 / Replication protein A 69 kDa DNA- binding subunit


Mass: 13265.821 Da / Num. of mol.: 1 / Fragment: DNA binding domain A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RFA1 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS / References: UniProt: P22336

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY
NMR detailsText: The chemical shift assignments were done with triple-resonance experiments. Restraints were get from 3D 13C, 15N NOESY data.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM scRPA DBD A U-15N, 13C; 20mM Sodium Phosphate, 100mM NaCl, 2mM DTT, pH 7.0; 90% H2O, 10% D2O90% H2O/10% D2O
21mM scRPA DBD A U-15N; 20mM Sodium Phosphate, 100mM NaCl, 2mM DTT, pH 7.0; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 7 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipelatestDelaglio et al.processing
VNMRlatestVarian, Inc.collection
X-PLORNIH 2.9.6Clore et al.,structure solution
X-PLORNIH 2.9.6Clore et al.,refinement
RefinementMethod: Torsional Angle Dynamics with Internal Variable Module
Software ordinal: 1
Details: The structure calculations were performed using 1138 interproton distance restraints and 161 dihedral angle restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 22

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