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Yorodumi- PDB-4nb3: Crystal structure of RPA70N in complex with a 3,4 dichlorophenyla... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nb3 | |||||||||
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Title | Crystal structure of RPA70N in complex with a 3,4 dichlorophenylalanine ATRIP derived peptide | |||||||||
Components |
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Keywords | PEPTIDE 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 / chromatin-protein adaptor activity / single-stranded telomeric DNA binding / regulation of double-strand break repair / Removal of the Flap Intermediate / Activation of the pre-replicative complex / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) ...ATR-ATRIP complex / protein localization to chromosome / DNA replication factor A complex / chromatin-protein adaptor activity / single-stranded telomeric DNA binding / regulation of double-strand break repair / Removal of the Flap Intermediate / Activation of the pre-replicative complex / 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 / nucleobase-containing compound metabolic process / Activation of ATR in response to replication stress / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / K63-linked polyubiquitin modification-dependent protein binding / site of DNA damage / Presynaptic phase of homologous DNA pairing and strand exchange / telomere maintenance via telomerase / Regulation of HSF1-mediated heat shock response / PCNA-Dependent Long Patch Base Excision Repair / HSF1 activation / meiotic cell cycle / mismatch repair / 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 recombination / DNA damage checkpoint signaling / nucleotide-excision repair / Fanconi Anemia Pathway / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / G2/M DNA damage checkpoint / Translesion Synthesis by POLH / double-strand break repair via homologous recombination / base-excision repair / HDR through Homologous Recombination (HRR) / PML body / Dual Incision in GG-NER / 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 / Processing of DNA double-strand break ends / site of double-strand break / single-stranded DNA binding / chromosome, telomeric region / DNA replication / Regulation of TP53 Activity through Phosphorylation / DNA recombination / damaged DNA binding / 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: 1.35 Å | |||||||||
Authors | Feldkamp, 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. | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nb3.cif.gz | 139.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nb3.ent.gz | 110.5 KB | Display | PDB format |
PDBx/mmJSON format | 4nb3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nb3_validation.pdf.gz | 437.4 KB | Display | wwPDB validaton report |
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Full document | 4nb3_full_validation.pdf.gz | 439.9 KB | Display | |
Data in XML | 4nb3_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 4nb3_validation.cif.gz | 28.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/4nb3 ftp://data.pdbj.org/pub/pdb/validation_reports/nb/4nb3 | HTTPS FTP |
-Related structure data
Related structure data | 4picS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | 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 | 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.15 % |
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Crystal grow | Temperature: 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 |
-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: MAR scanner 300 mm plate / Detector: IMAGE PLATE |
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: 1.35→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 shell | Resolution: 1.35→1.4 Å / % possible all: 91.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4PIC Resolution: 1.35→26.17 Å / SU ML: 0.11 / σ(F): 1.35 / Phase error: 15.73 / 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: 1.35→26.17 Å
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Refine LS restraints |
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LS refinement shell |
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