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- PDB-4r4t: Crystal Structure of RPA70N in complex with 5-(4-((4-(5-carboxyfu... -

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Basic information

Entry
Database: PDB / ID: 4r4t
TitleCrystal Structure of RPA70N in complex with 5-(4-((4-(5-carboxyfuran-2-yl)phenylthioamido)methyl)phenyl)-1-(3,4-dichlorophenyl)-1H-pyrazole-3-carboxylic acid
ComponentsReplication protein A 70 kDa DNA-binding subunit
KeywordsPROTEIN BINDING / OB-fold / Protein-Protein Interaction
Function / homology
Function and homology information


protein localization to chromosome / DNA replication factor A complex / lateral element / single-stranded telomeric DNA binding / G-rich strand telomeric DNA binding / Removal of the Flap Intermediate / chromatin-protein adaptor activity / protein localization to site of double-strand break / 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 / lateral element / single-stranded telomeric DNA binding / G-rich strand telomeric DNA binding / Removal of the Flap Intermediate / chromatin-protein adaptor activity / protein localization to site of double-strand break / 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 / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / hemopoiesis / Presynaptic phase of homologous DNA pairing and strand exchange / site of DNA damage / PCNA-Dependent Long Patch Base Excision Repair / Regulation of HSF1-mediated heat shock response / Activation of the pre-replicative complex / HSF1 activation / telomere maintenance via telomerase / mismatch repair / Activation of ATR in response to replication stress / SUMOylation of DNA damage response and repair proteins / homeostasis of number of cells within a tissue / 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 / male germ cell nucleus / nucleotide-excision repair / Fanconi Anemia Pathway / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / double-strand break repair via homologous recombination / base-excision repair / PML body / G2/M DNA damage checkpoint / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / Meiotic recombination / DNA-templated DNA replication / 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 / site of double-strand break / Processing of DNA double-strand break ends / DNA recombination / Regulation of TP53 Activity through Phosphorylation / in utero embryonic development / damaged DNA binding / chromosome, telomeric region / DNA replication / DNA repair / positive regulation of cell population proliferation / DNA damage response / chromatin binding / zinc ion binding / nucleoplasm / 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
Chem-3J0 / Replication protein A 70 kDa DNA-binding subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsFeldkamp, M.D. / Waterson, A.G. / Kennedy, J.P. / Patrone, J.D. / Pelz, N.F. / Frank, A.O. / Vangamudi, B. / Sousa-Fagundes, E.M. / Rossanese, O.W. / Fesik, S.W. / Chazin, W.J.
CitationJournal: ACS Med Chem Lett / Year: 2015
Title: Diphenylpyrazoles as replication protein a inhibitors.
Authors: Waterson, A.G. / Kennedy, J.P. / Patrone, J.D. / Pelz, N.F. / Feldkamp, M.D. / Frank, A.O. / Vangamudi, B. / Souza-Fagundes, E.M. / Rossanese, O.W. / Chazin, W.J. / Fesik, S.W.
History
DepositionAug 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Replication protein A 70 kDa DNA-binding subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0902
Polymers13,4981
Non-polymers5921
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.190, 53.920, 54.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Replication protein A 70 kDa DNA-binding subunit / RP-A p70 / Replication factor A protein 1 / RF-A protein 1 / Single-stranded DNA-binding protein / ...RP-A p70 / Replication factor A protein 1 / RF-A protein 1 / Single-stranded DNA-binding protein / Replication protein A 70 kDa DNA-binding subunit / N-terminally processed


Mass: 13497.728 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-120) / Mutation: E7R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPA1, REPA1, RPA70 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P27694
#2: Chemical ChemComp-3J0 / 5-{4-[({[4-(5-carboxyfuran-2-yl)phenyl]carbonothioyl}amino)methyl]phenyl}-1-(3,4-dichlorophenyl)-1H-pyrazole-3-carboxylic acid


Mass: 592.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H19Cl2N3O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.41 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM MES, 200 mM Calcium Acetate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 19, 2012
RadiationMonochromator: Si(100) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.28→27.01 Å / Num. obs: 35763 / % possible obs: 99.84 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 19.4 Å2 / Rsym value: 0.043 / Net I/σ(I): 18.13
Reflection shellResolution: 1.28→1.33 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.72 / Rsym value: 0.457 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.9_1692)model building
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4IPC

4ipc


Resolution: 1.28→27.007 Å / SU ML: 0.11 / σ(F): 1.34 / Phase error: 16.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1747 1497 5.09 %
Rwork0.1391 --
obs0.1409 29414 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.28→27.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms938 0 40 120 1098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011070
X-RAY DIFFRACTIONf_angle_d1.4431473
X-RAY DIFFRACTIONf_dihedral_angle_d19.86445
X-RAY DIFFRACTIONf_chiral_restr0.082173
X-RAY DIFFRACTIONf_plane_restr0.006191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.32130.20211610.17972479X-RAY DIFFRACTION100
1.3213-1.36860.23631430.16532467X-RAY DIFFRACTION100
1.3686-1.42330.19641210.15182536X-RAY DIFFRACTION100
1.4233-1.48810.19171300.13922496X-RAY DIFFRACTION100
1.4881-1.56660.21271220.13052522X-RAY DIFFRACTION100
1.5666-1.66470.14711390.12132521X-RAY DIFFRACTION100
1.6647-1.79320.15341500.11312501X-RAY DIFFRACTION100
1.7932-1.97360.14231320.10782529X-RAY DIFFRACTION100
1.9736-2.25910.1511400.11072573X-RAY DIFFRACTION100
2.2591-2.84570.18181300.14162596X-RAY DIFFRACTION100
2.8457-27.01310.18481290.16152697X-RAY DIFFRACTION99

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