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Yorodumi- PDB-4r4c: Structure of RPA70N in complex with 5-(4-((4-(5-carboxyfuran-2-yl... -
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-Basic information
Entry | Database: PDB / ID: 4r4c | ||||||
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Title | Structure of RPA70N in complex with 5-(4-((4-(5-carboxyfuran-2-yl)-2-chlorobenzamido)methyl)phenyl)-1-(3,4-dichlorophenyl)-1H-pyrazole-3-carboxylic acid | ||||||
Components | Replication protein A 70 kDa DNA-binding subunit | ||||||
Keywords | PROTEIN BINDING / OB-Fold / Protein-Protein Interaction | ||||||
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 / single-stranded DNA binding / site of double-strand break / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Feldkamp, 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. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r4c.cif.gz | 88.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r4c.ent.gz | 68.3 KB | Display | PDB format |
PDBx/mmJSON format | 4r4c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4r4c_validation.pdf.gz | 694 KB | Display | wwPDB validaton report |
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Full document | 4r4c_full_validation.pdf.gz | 694 KB | Display | |
Data in XML | 4r4c_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 4r4c_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/4r4c ftp://data.pdbj.org/pub/pdb/validation_reports/r4/4r4c | HTTPS FTP |
-Related structure data
Related structure data | 4r4iC 4r4oC 4r4qC 4r4tC 4ipcS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-3HS / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 21, 2012 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 22271 / % possible obs: 99.38 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 19.9 Å2 / Rsym value: 0.062 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 3.29 / Num. unique all: 2181 / Rsym value: 0.425 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4IPC Resolution: 1.4→31.089 Å / SU ML: 0.12 / σ(F): 1.34 / Phase error: 17.09 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→31.089 Å
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Refine LS restraints |
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LS refinement shell |
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