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- PDB-4nb3: Crystal structure of RPA70N in complex with a 3,4 dichlorophenyla... -

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Basic information

Entry
Database: PDB / ID: 4nb3
TitleCrystal structure of RPA70N in complex with a 3,4 dichlorophenylalanine ATRIP derived peptide
Components
  • 3,4 dichlorophenylalanine ATRIP derived peptide
  • Replication protein A 70 kDa DNA-binding subunit
KeywordsPEPTIDE BINDING PROTEIN / OB fold / Protein-Protein Interaction / 3 / 4 dichlorophenylalanine
Function / homology
Function and homology information


ATR-ATRIP complex / protein localization to chromosome / DNA replication factor A complex / single-stranded telomeric DNA binding / lateral element / G-rich strand telomeric DNA binding / chromatin-protein adaptor activity / protein localization to site of double-strand break / Removal of the Flap Intermediate / regulation of double-strand break repair ...ATR-ATRIP complex / protein localization to chromosome / DNA replication factor A complex / single-stranded telomeric DNA binding / lateral element / G-rich strand telomeric DNA binding / chromatin-protein adaptor activity / protein localization to site of double-strand break / Removal of the Flap Intermediate / regulation of double-strand break repair / 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 / nucleobase-containing compound metabolic process / HDR through Single Strand Annealing (SSA) / K63-linked polyubiquitin modification-dependent protein binding / Impaired BRCA2 binding to RAD51 / hemopoiesis / site of DNA damage / Presynaptic phase of homologous DNA pairing and strand exchange / PCNA-Dependent Long Patch Base Excision Repair / Activation of the pre-replicative complex / Regulation of HSF1-mediated heat shock response / HSF1 activation / telomere maintenance via telomerase / mismatch repair / SUMOylation of DNA damage response and repair proteins / Activation of ATR in response to replication stress / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / homeostasis of number of cells within a tissue / telomere maintenance / Fanconi Anemia Pathway / DNA damage checkpoint signaling / male germ cell nucleus / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / meiotic cell cycle / Translesion Synthesis by POLH / double-strand break repair via homologous recombination / nucleotide-excision repair / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / G2/M DNA damage checkpoint / PML body / base-excision repair / Meiotic recombination / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA-templated DNA replication / site of double-strand break / single-stranded DNA binding / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / DNA recombination / damaged DNA binding / in utero embryonic development / 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
ATR-interacting protein / 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 ...ATR-interacting protein / 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
Replication protein A 70 kDa DNA-binding subunit / ATR-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsFeldkamp, M.D. / Frank, A.O. / Vangamudi, B. / Souza-Fagundes, E.M. / Luzwik, J.W. / Cortez, D. / Olejniczak, O.T. / Waterson, A.G. / Rossanese, O.W. / Fesik, S.W. / Chazin, W.J.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Discovery of a Potent Stapled Helix Peptide That Binds to the 70N Domain of Replication Protein A.
Authors: Frank, A.O. / Vangamudi, B. / Feldkamp, M.D. / Souza-Fagundes, E.M. / Luzwick, J.W. / Cortez, D. / Olejniczak, E.T. / Waterson, A.G. / Rossanese, O.W. / Chazin, W.J. / Fesik, S.W.
History
DepositionOct 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: 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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Jul 10, 2024Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
B: Replication protein A 70 kDa DNA-binding subunit
C: 3,4 dichlorophenylalanine ATRIP derived peptide
D: 3,4 dichlorophenylalanine ATRIP derived peptide


Theoretical massNumber of molelcules
Total (without water)31,4284
Polymers31,4284
Non-polymers00
Water8,161453
1
A: Replication protein A 70 kDa DNA-binding subunit
C: 3,4 dichlorophenylalanine ATRIP derived peptide


Theoretical massNumber of molelcules
Total (without water)15,7142
Polymers15,7142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Replication protein A 70 kDa DNA-binding subunit
D: 3,4 dichlorophenylalanine ATRIP derived peptide


Theoretical massNumber of molelcules
Total (without water)15,7142
Polymers15,7142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.145, 46.803, 78.792
Angle α, β, γ (deg.)90.00, 120.64, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-396-

HOH

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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.: 2 / 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: Protein/peptide 3,4 dichlorophenylalanine ATRIP derived peptide


Mass: 2216.161 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Synthesized peptide contains a covalently attached fluorescein isothiocyanate (FITC) at its N-terminus and a 3,4 dichlorophenylalanine incorporated into the peptide chain at position 15
References: UniProt: Q8WXE1*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 46.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM Bis-Tris, 200 mM ammonium acetate, 25% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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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
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.35→26.17 Å / Num. obs: 60645 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Net I/σ(I): 11.57
Reflection shellResolution: 1.35→1.4 Å / % possible all: 91.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.8.2_1309)model building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.2_1309phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4PIC

4pic


Resolution: 1.35→26.17 Å / SU ML: 0.11 / σ(F): 1.35 / Phase error: 15.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1747 3095 5.1 %RANDOM
Rwork0.1442 ---
obs0.1457 60645 97.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→26.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2171 0 0 453 2624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182454
X-RAY DIFFRACTIONf_angle_d1.9353385
X-RAY DIFFRACTIONf_dihedral_angle_d15.5861007
X-RAY DIFFRACTIONf_chiral_restr0.127388
X-RAY DIFFRACTIONf_plane_restr0.01438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.37170.23781270.17622463X-RAY DIFFRACTION91
1.3717-1.39420.21641430.16832626X-RAY DIFFRACTION100
1.3942-1.41820.20171330.15622705X-RAY DIFFRACTION100
1.4182-1.4440.24781380.15212643X-RAY DIFFRACTION100
1.444-1.47180.18331470.1472655X-RAY DIFFRACTION100
1.4718-1.50180.16971580.13552677X-RAY DIFFRACTION100
1.5018-1.53450.2071250.12692666X-RAY DIFFRACTION100
1.5345-1.57020.17541600.12022644X-RAY DIFFRACTION100
1.5702-1.60940.18331570.12272684X-RAY DIFFRACTION100
1.6094-1.65290.15811330.11732644X-RAY DIFFRACTION100
1.6529-1.70160.17011380.12192701X-RAY DIFFRACTION100
1.7016-1.75650.14871660.12572663X-RAY DIFFRACTION100
1.7565-1.81920.20091350.13012662X-RAY DIFFRACTION100
1.8192-1.89210.18051360.13642681X-RAY DIFFRACTION100
1.8921-1.97810.16671560.13712596X-RAY DIFFRACTION98
1.9781-2.08240.15451580.1322661X-RAY DIFFRACTION100
2.0824-2.21280.16471370.14272715X-RAY DIFFRACTION100
2.2128-2.38350.17461320.14242562X-RAY DIFFRACTION95
2.3835-2.62320.17261440.14812690X-RAY DIFFRACTION100
2.6232-3.00230.18211280.15992731X-RAY DIFFRACTION100
3.0023-3.78080.16831220.1442308X-RAY DIFFRACTION87
3.7808-26.17480.1751220.16092173X-RAY DIFFRACTION95

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