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- PDB-8c3j: Stapled peptide SP2 in complex with humanised RadA mutant HumRadA22 -
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Open data
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Basic information
Entry | Database: PDB / ID: 8c3j | ||||||
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Title | Stapled peptide SP2 in complex with humanised RadA mutant HumRadA22 | ||||||
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![]() | RECOMBINATION / Stapled peptide / Rad51 / BRCA2 / BRC repeat | ||||||
Function / homology | ![]() BRCA2-MAGE-D1 complex / negative regulation of mammary gland epithelial cell proliferation / mitotic recombination-dependent replication fork processing / establishment of protein localization to telomere / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / nuclear ubiquitin ligase complex / lateral element / telomere maintenance via recombination / DNA recombinase assembly ...BRCA2-MAGE-D1 complex / negative regulation of mammary gland epithelial cell proliferation / mitotic recombination-dependent replication fork processing / establishment of protein localization to telomere / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / nuclear ubiquitin ligase complex / lateral element / telomere maintenance via recombination / DNA recombinase assembly / histone H4 acetyltransferase activity / histone H3 acetyltransferase activity / regulation of DNA damage checkpoint / mitotic recombination / Impaired BRCA2 binding to PALB2 / DNA strand invasion / HDR through MMEJ (alt-NHEJ) / gamma-tubulin binding / DNA strand exchange activity / DNA repair complex / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / response to UV-C / oocyte maturation / Resolution of D-loop Structures through Holliday Junction Intermediates / inner cell mass cell proliferation / ATP-dependent DNA damage sensor activity / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / hematopoietic stem cell proliferation / Impaired BRCA2 binding to RAD51 / female gonad development / male meiosis I / Presynaptic phase of homologous DNA pairing and strand exchange / centrosome duplication / response to X-ray / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of mitotic cell cycle / regulation of cytokinesis / secretory granule / cellular response to ionizing radiation / nucleotide-excision repair / response to gamma radiation / double-strand break repair via homologous recombination / HDR through Homologous Recombination (HRR) / brain development / Meiotic recombination / cellular senescence / double-strand break repair / single-stranded DNA binding / spermatogenesis / double-stranded DNA binding / protease binding / chromosome, telomeric region / damaged DNA binding / centrosome / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / ATP hydrolysis activity / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pantelejevs, T. / Hyvonen, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A recombinant approach for stapled peptide discovery yields inhibitors of the RAD51 recombinase. Authors: Pantelejevs, T. / Zuazua-Villar, P. / Koczy, O. / Counsell, A.J. / Walsh, S.J. / Robertson, N.S. / Spring, D.R. / Downs, J.A. / Hyvonen, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.3 KB | Display | ![]() |
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PDB format | ![]() | 81.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 711.2 KB | Display | ![]() |
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Full document | ![]() | 716.4 KB | Display | |
Data in XML | ![]() | 18.4 KB | Display | |
Data in CIF | ![]() | 24.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8br9C ![]() 8c3nC ![]() 6hquS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25542.064 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 3687.163 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-TKI / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.23 Å3/Da / Density % sol: 70.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Protein in 20 mM CHES pH 9.5, 100 mM NaCl. Condition: 8 % w/v PEG 8000 (precipitant) 0.08 M Potassium phosphate pH 5.6 (buffer) 200:200 uL drop |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.02→87.92 Å / Num. obs: 18416 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 89.08 Å2 / CC1/2: 1 / Rrim(I) all: 0.242 / Net I/σ(I): 10 |
Reflection shell | Resolution: 3.02→3.07 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 13512 / CC1/2: 0.3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6HQU Resolution: 3.02→87.92 Å / SU ML: 0.4747 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.7701 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 91.23 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.02→87.92 Å
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Refine LS restraints |
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LS refinement shell |
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