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- PDB-5e7n: Crystal Structure of RPA70N in complex with VU0085636 -

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Basic information

Entry
Database: PDB / ID: 5e7n
TitleCrystal Structure of RPA70N in complex with VU0085636
ComponentsReplication protein A 70 kDa DNA-binding subunit
KeywordsPROTEIN BINDING/INHIBITOR / Inhibitor / Complex / PROTEIN BINDING-INHIBITOR complex
Function / homology
Function and homology information


protein localization to chromosome / DNA replication factor A complex / chromatin-protein adaptor activity / 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) / protein localization to site of double-strand break / 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 / 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) / protein localization to site of double-strand break / 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 / PCNA-Dependent Long Patch Base Excision Repair / HSF1 activation / Regulation of HSF1-mediated heat shock response / Activation of the pre-replicative complex / 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 / G2/M DNA damage checkpoint / HDR through Homologous Recombination (HRR) / PML body / Dual Incision in GG-NER / DNA-templated DNA replication / 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 / nucleus / metal ion binding
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-5KR / Replication protein A 70 kDa DNA-binding subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsGilston, B.A. / Patrone, J.D. / Pelz, N.F. / Bates, B.S. / Souza-Fagundes, E.M. / Vangamudi, B. / Camper, D. / Kuznetsov, A. / Browning, C.F. / Feldkamp, M.D. ...Gilston, B.A. / Patrone, J.D. / Pelz, N.F. / Bates, B.S. / Souza-Fagundes, E.M. / Vangamudi, B. / Camper, D. / Kuznetsov, A. / Browning, C.F. / Feldkamp, M.D. / Olejniczak, E.T. / Rossanese, O.W. / Waterson, A.G. / Fesik, S.W. / Chazin, W.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM065484 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)5DP1OD006933/8DP1CA174419 United States
CitationJournal: Chemmedchem / Year: 2016
Title: Identification and Optimization of Anthranilic Acid Based Inhibitors of Replication Protein A.
Authors: Patrone, J.D. / Pelz, N.F. / Bates, B.S. / Souza-Fagundes, E.M. / Vangamudi, B. / Camper, D.V. / Kuznetsov, A.G. / Browning, C.F. / Feldkamp, M.D. / Frank, A.O. / Gilston, B.A. / Olejniczak, ...Authors: Patrone, J.D. / Pelz, N.F. / Bates, B.S. / Souza-Fagundes, E.M. / Vangamudi, B. / Camper, D.V. / Kuznetsov, A.G. / Browning, C.F. / Feldkamp, M.D. / Frank, A.O. / Gilston, B.A. / Olejniczak, E.T. / Rossanese, O.W. / Waterson, A.G. / Chazin, W.J. / Fesik, S.W.
History
DepositionOct 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)13,9872
Polymers13,4981
Non-polymers4891
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.560, 53.260, 54.480
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


Mass: 13497.728 Da / Num. of mol.: 1 / Fragment: 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) / References: UniProt: P27694
#2: Chemical ChemComp-5KR / 2-({3-[(4-bromophenyl)sulfamoyl]-4-methylbenzoyl}amino)benzoic acid


Mass: 489.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H17BrN2O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.65 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM MES, 200 mM Calcium Acetate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 5, 2012
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.21→31.47 Å / Num. obs: 34513 / % possible obs: 99.8 % / Redundancy: 5.8 % / Net I/σ(I): 22.49

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000708data reduction
HKL-2000708data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R4T

4r4t


Resolution: 1.21→31.47 Å / SU ML: 0.14 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 21.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2155 1740 5.04 %
Rwork0.1959 --
obs0.1968 34513 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.21→31.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms942 0 30 70 1042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061049
X-RAY DIFFRACTIONf_angle_d1.2061434
X-RAY DIFFRACTIONf_dihedral_angle_d12.98417
X-RAY DIFFRACTIONf_chiral_restr0.066167
X-RAY DIFFRACTIONf_plane_restr0.005186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.24560.35261500.31512513X-RAY DIFFRACTION93
1.2456-1.28580.25461540.24642673X-RAY DIFFRACTION99
1.2858-1.33180.24781490.22962742X-RAY DIFFRACTION100
1.3318-1.38510.23791230.2192717X-RAY DIFFRACTION100
1.3851-1.44810.21151380.21252731X-RAY DIFFRACTION100
1.4481-1.52450.22291650.20242735X-RAY DIFFRACTION100
1.5245-1.620.19861550.19712728X-RAY DIFFRACTION100
1.62-1.74510.21971370.19022765X-RAY DIFFRACTION100
1.7451-1.92070.2031380.18492760X-RAY DIFFRACTION100
1.9207-2.19850.17111450.16882785X-RAY DIFFRACTION100
2.1985-2.76970.20741510.18442828X-RAY DIFFRACTION100
2.7697-31.48470.22891350.19842796X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -7.2183 Å / Origin y: -8.1622 Å / Origin z: 11.2021 Å
111213212223313233
T0.068 Å20.0095 Å2-0.011 Å2-0.0705 Å2-0.0097 Å2--0.0772 Å2
L1.257 °2-0.1636 °2-0.3291 °2-1.2529 °20.1106 °2--2.0075 °2
S0.0212 Å °-0.0466 Å °-0.0268 Å °0.0952 Å °0.004 Å °-0.0084 Å °0.0103 Å °-0.0378 Å °-0.0242 Å °
Refinement TLS groupSelection details: all

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