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- PDB-1z1d: Structural Model for the interaction between RPA32 C-terminal dom... -

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Basic information

Entry
Database: PDB / ID: 1z1d
TitleStructural Model for the interaction between RPA32 C-terminal domain and SV40 T antigen origin binding domain.
Components
  • Large T antigen
  • Replication protein A 32 kDa subunit
KeywordsREPLICATION / Winged Helix-turn-Helix motif / Origin binding domain / Protein-Protein Complex
Function / homology
Function and homology information


protein localization to chromosome / DNA replication factor A complex / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / regulation of DNA damage checkpoint / G-rich strand telomeric DNA binding / bidirectional double-stranded viral DNA replication / Removal of the Flap Intermediate / Removal of the Flap Intermediate from the C-strand / 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 / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / regulation of DNA damage checkpoint / G-rich strand telomeric DNA binding / bidirectional double-stranded viral DNA replication / Removal of the Flap Intermediate / Removal of the Flap Intermediate from the C-strand / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / viral DNA genome replication / DNA 3'-5' helicase / HDR through Single Strand Annealing (SSA) / regulation of double-strand break repair via homologous recombination / Impaired BRCA2 binding to RAD51 / telomeric DNA binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / Presynaptic phase of homologous DNA pairing and strand exchange / DNA replication origin binding / PCNA-Dependent Long Patch Base Excision Repair / Activation of the pre-replicative complex / Regulation of HSF1-mediated heat shock response / HSF1 activation / mismatch repair / Activation of ATR in response to replication stress / mitotic G1 DNA damage checkpoint signaling / telomere maintenance / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / isomerase activity / nucleotide-excision repair / helicase activity / Fanconi Anemia Pathway / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / double-strand break repair via homologous recombination / Translesion Synthesis by POLH / G2/M DNA damage checkpoint / base-excision repair / PML body / Meiotic recombination / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / 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 / double-stranded DNA binding / protein phosphatase binding / symbiont-mediated perturbation of host ubiquitin-like protein modification / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / chromosome, telomeric region / DNA replication / nuclear body / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ubiquitin protein ligase binding / chromatin / host cell nucleus / enzyme binding / ATP hydrolysis activity / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus
Similarity search - Function
Replication factor A protein 2 / Replication protein A, C-terminal / Replication protein A C terminal / Replication Protein E1; Chain: A, - #20 / Replication factor A protein-like / Replication Protein E1; Chain: A, / Large T antigen, polyomaviridae / Large T antigen, polyomavirus, C-terminal / Zinc finger, large T-antigen D1-type / Origin of replication binding protein ...Replication factor A protein 2 / Replication protein A, C-terminal / Replication protein A C terminal / Replication Protein E1; Chain: A, - #20 / Replication factor A protein-like / Replication Protein E1; Chain: A, / Large T antigen, polyomaviridae / Large T antigen, polyomavirus, C-terminal / Zinc finger, large T-antigen D1-type / Origin of replication binding protein / Polyomavirus large T antigen C-terminus / Large T-antigen (T-ag) origin-binding domain (OBD) profile. / Zinc finger large T-antigen (T-ag) D1-type profile. / T antigen, Ori-binding / Zinc finger, large T-antigen D1 domain superfamily / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / 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 / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Large T antigen / Replication protein A 32 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
Simian virus 40
MethodSOLUTION NMR / Rigid body docking, Semi-flexible simulated annealing, Refinement using explicit water
AuthorsArunkumar, A.I. / Klimovich, V. / Jiang, X. / Ott, R.D. / Mizoue, L. / Fanning, E. / Chazin, W.J.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Insights into hRPA32 C-terminal domain--mediated assembly of the simian virus 40 replisome.
Authors: Arunkumar, A.I. / Klimovich, V. / Jiang, X. / Ott, R.D. / Mizoue, L. / Fanning, E. / Chazin, W.J.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2000
Title: Structural basis for the recognition of DNA repair proteins UNG2, XPA, and RAD52 by replication factor A
Authors: Mer, G. / Bochkarev, A. / Gupta, R. / Bochkareva, E. / Frappier, L. / Ingles, C.M. / Edwards, A.M. / Chazin, W.J.
#2: Journal: Nat.Struct.Mol.Biol. / Year: 1996
Title: Solution structure of the origin DNA binding domain of SV40 T antigen
Authors: Luo, X. / Sanford, D.G. / Bullock, P.A. / Bachovchin, W.W.
History
DepositionMar 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2005Provider: 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: 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 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Replication protein A 32 kDa subunit
B: Large T antigen


Theoretical massNumber of molelcules
Total (without water)26,1102
Polymers26,1102
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)20 / 200structures with acceptable covalent geometry,structures with favorable non-bond energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Replication protein A 32 kDa subunit / RP-A / RF-A / Replication factor-A protein 2 / RPA32


Mass: 10999.127 Da / Num. of mol.: 1 / Fragment: RPA32 C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPA2, REPA2, RPA32 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P15927
#2: Protein Large T antigen / SV40 T antigen


Mass: 15111.362 Da / Num. of mol.: 1 / Fragment: SV40 T antigen Origin binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian virus 40 / Genus: Polyomavirus / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03070

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 15N-1H HSQC
1222D 15N-1H HSQC
NMR detailsText: This model structure was obtained using ambigous chemical shift pertubation constraints and validated using residual dipolar couplings and point mutations on the interface

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2mM RPA32C U-15N, 0.6mM Tag-OBD, 20mM Tris buffer pH 7.0, 2 mM DTT, 5mM MgCl2, 90% H2O, 10% D2O90% H2O/10% D2O
20.2mM Tag-OBD U-15N, 0.6mM RPA32C, 20mM Tris buffer pH 7.0, 2mM DTT, 5mM MgCl2, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 0.03 M / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
UXNMR2.3Bruker softwarecollection
Felix2000Accelrys, Incdata analysis
HADDOCK1.3Bonvin, A.M.structure solution
HADDOCK1.3Bonvin, A.M.refinement
RefinementMethod: Rigid body docking, Semi-flexible simulated annealing, Refinement using explicit water
Software ordinal: 1
Details: 1500 conformers were obtained in the rigid body docking and 200 best conformers were selected for semi-flexible simulated annealing followed by refinement.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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