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- PDB-1dpu: SOLUTION STRUCTURE OF THE C-TERMINAL DOMAIN OF HUMAN RPA32 COMPLE... -

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Basic information

Entry
Database: PDB / ID: 1dpu
TitleSOLUTION STRUCTURE OF THE C-TERMINAL DOMAIN OF HUMAN RPA32 COMPLEXED WITH UNG2(73-88)
Components
  • REPLICATION PROTEIN A (RPA32) C-TERMINAL DOMAIN
  • URACIL DNA GLYCOSYLASE (UNG2)
KeywordsDNA BINDING PROTEIN / PROTEIN-PEPTIDE COMPLEX / DNA REPAIR
Function / homology
Function and homology information


protein localization to chromosome / DNA replication factor A complex / base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / regulation of DNA damage checkpoint / Removal of the Flap Intermediate / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) ...protein localization to chromosome / DNA replication factor A complex / base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / regulation of DNA damage checkpoint / Removal of the Flap Intermediate / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / isotype switching / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding / uracil DNA N-glycosylase activity / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / regulation of double-strand break repair via homologous recombination / telomeric DNA binding / Presynaptic phase of homologous DNA pairing and strand exchange / ribosomal small subunit binding / PCNA-Dependent Long Patch Base Excision Repair / HSF1 activation / Regulation of HSF1-mediated heat shock response / Activation of the pre-replicative complex / somatic hypermutation of immunoglobulin genes / mismatch repair / Activation of ATR in response to replication stress / mitotic G1 DNA damage checkpoint signaling / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere maintenance / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Chromatin modifications during the maternal to zygotic transition (MZT) / 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 / G2/M DNA damage checkpoint / HDR through Homologous Recombination (HRR) / PML body / Dual Incision in GG-NER / Meiotic recombination / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / single-stranded DNA binding / Processing of DNA double-strand break ends / protein phosphatase binding / Regulation of TP53 Activity through Phosphorylation / DNA replication / damaged DNA binding / chromosome, telomeric region / nuclear body / ubiquitin protein ligase binding / chromatin / negative regulation of apoptotic process / enzyme binding / mitochondrion / nucleoplasm / nucleus
Similarity search - Function
Replication factor A protein 2 / Replication protein A, C-terminal / Replication protein A C terminal / Replication factor A protein-like / Uracil-DNA glycosylase family 1 / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA glycosylase-like ...Replication factor A protein 2 / Replication protein A, C-terminal / Replication protein A C terminal / Replication factor A protein-like / Uracil-DNA glycosylase family 1 / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Uracil-DNA glycosylase / Replication protein A 32 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY SIMULATED ANNEALING
AuthorsMer, G. / Edwards, A.M. / Chazin, W.J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: Structural basis for the recognition of DNA repair proteins UNG2, XPA, and RAD52 by replication factor RPA.
Authors: Mer, G. / Bochkarev, A. / Gupta, R. / Bochkareva, E. / Frappier, L. / Ingles, C.J. / Edwards, A.M. / Chazin, W.J.
History
DepositionDec 27, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 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: 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 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: REPLICATION PROTEIN A (RPA32) C-TERMINAL DOMAIN
B: URACIL DNA GLYCOSYLASE (UNG2)


Theoretical massNumber of molelcules
Total (without water)12,4122
Polymers12,4122
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)30 / 50structures with the least restraint violations
RepresentativeModel #1

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Components

#1: Protein REPLICATION PROTEIN A (RPA32) C-TERMINAL DOMAIN


Mass: 10585.656 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN (RESIDUES 172-270)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: P15927
#2: Protein/peptide URACIL DNA GLYCOSYLASE (UNG2)


Mass: 1826.222 Da / Num. of mol.: 1 / Fragment: RESIDUES 73-88 / Source method: obtained synthetically
Details: THIS PEPTIDE SEQUENCE IS FOUND IN THE NUCLEAR [UNG2(73-88)] AND MITOCHONDRIAL [UNG1(64-79)] FORMS OF HUMAN URACIL-DNA GLYCOSYLASE
References: UniProt: P13051

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 13C- SEPARATED NOESY
1313D 15N- SEPARATED NOESY
141DQF- COSY
151HNHA
161HNHB
171HACAHB -COSY
181FILTER-EDITED NOESY
191DOUBLE-HALF FILTERED NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING DOUBLE- AND TRIPLE-RESONANCE NMR SPECTROSCOPY ***

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Sample preparation

DetailsContents: 1MM RPA32(172-270) U- 15N,13C; 1.2 MM UNG2(73- 88) NA; 25MM PHOSPHATE BUFFER NA; 50MM NACL; 5 MM DTT NA
Sample conditionsIonic strength: 25mM PHOSPHATE, 50mM NACL / pH: 7 / Pressure: AMBIENT / Temperature: 298.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker DRXBrukerDRX6002
Bruker DMXBrukerDMX7503
Bruker DMXBrukerDMX8004

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Processing

NMR software
NameVersionDeveloperClassification
DIANA2.8GUNTERT PROGRAM 2 : AMBER 4.1 AUTHORS 2 : PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMANrefinement
MSI FELIX97 SOFTWARE USED 2 : DIANA 2.8 SOFTWARE USED 3 : AMBER4.1structure solution
RefinementMethod: DISTANCE GEOMETRY SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 30

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