- PDB-3al3: Crystal Structure of TopBP1 BRCT7/8-BACH1 peptide complex -
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Basic information
Entry
Database: PDB / ID: 3al3
Title
Crystal Structure of TopBP1 BRCT7/8-BACH1 peptide complex
Components
DNA topoisomerase 2-binding protein 1
Peptide of Fanconi anemia group J protein
Keywords
DNA BINDING PROTEIN/PROTEIN BINDING / BRCT domain-phosphopeptide complex / DNA BINDING PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information
meiotic DNA double-strand break processing involved in reciprocal meiotic recombination / cellular response to vitamin / chiasma assembly / broken chromosome clustering / catalytic activity, acting on a nucleic acid / spermatogonial cell division / BRCA1-B complex / Cytosolic iron-sulfur cluster assembly / double-strand break repair involved in meiotic recombination / phosphorylation-dependent protein binding ...meiotic DNA double-strand break processing involved in reciprocal meiotic recombination / cellular response to vitamin / chiasma assembly / broken chromosome clustering / catalytic activity, acting on a nucleic acid / spermatogonial cell division / BRCA1-B complex / Cytosolic iron-sulfur cluster assembly / double-strand break repair involved in meiotic recombination / phosphorylation-dependent protein binding / homologous recombination / DNA replication checkpoint signaling / chromatin-protein adaptor activity / DNA 5'-3' helicase / Impaired BRCA2 binding to PALB2 / double-strand break repair via alternative nonhomologous end joining / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / protein-DNA covalent cross-linking repair / mitotic DNA replication checkpoint signaling / Homologous DNA Pairing and Strand Exchange / 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 / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / DNA metabolic process / response to ionizing radiation / Impaired BRCA2 binding to RAD51 / seminiferous tubule development / spermatid development / mitotic G2 DNA damage checkpoint signaling / site of DNA damage / Presynaptic phase of homologous DNA pairing and strand exchange / cellular response to angiotensin / DNA replication initiation / chromosome organization / DNA helicase activity / male germ cell nucleus / protein serine/threonine kinase activator activity / DNA damage checkpoint signaling / condensed nuclear chromosome / replication fork / isomerase activity / nucleotide-excision repair / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / PML body / HDR through Homologous Recombination (HRR) / response to toxic substance / spindle pole / double-strand break repair / actin cytoskeleton / site of double-strand break / chromosome / Processing of DNA double-strand break ends / 4 iron, 4 sulfur cluster binding / 5'-3' DNA helicase activity / cellular response to hypoxia / nuclear membrane / Regulation of TP53 Activity through Phosphorylation / RNA helicase activity / nuclear body / negative regulation of cell population proliferation / negative regulation of gene expression / DNA repair / centrosome / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / plasma membrane / cytoplasm Similarity search - Function
Resolution: 2.15→33.9 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2364 / WRfactor Rwork: 0.1956 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8292 / SU B: 12.379 / SU ML: 0.146 / SU R Cruickshank DPI: 0.2561 / SU Rfree: 0.1986 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2364
699
5 %
RANDOM
Rwork
0.1955
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-
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obs
0.1975
14021
99.86 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
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