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Yorodumi- PDB-1t29: Crystal structure of the BRCA1 BRCT repeats bound to a phosphoryl... -
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-Basic information
Entry | Database: PDB / ID: 1t29 | ||||||
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Title | Crystal structure of the BRCA1 BRCT repeats bound to a phosphorylated BACH1 peptide | ||||||
Components |
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Keywords | SIGNALING PROTEIN / BRCA1 / BRCT repeats / BACH1 / phosphopeptide recognition / breast cancer | ||||||
Function / homology | Function and homology information meiotic DNA double-strand break processing involved in reciprocal meiotic recombination / cellular response to vitamin / chiasma assembly / Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function / spermatogonial cell division / : / BRCA1-BARD1 complex / : / BRCA1-C complex ...meiotic DNA double-strand break processing involved in reciprocal meiotic recombination / cellular response to vitamin / chiasma assembly / Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function / spermatogonial cell division / : / BRCA1-BARD1 complex / : / BRCA1-C complex / BRCA1-B complex / BRCA1-A complex / random inactivation of X chromosome / negative regulation of centriole replication / gamma-tubulin ring complex / negative regulation of intracellular estrogen receptor signaling pathway / Cytosolic iron-sulfur cluster assembly / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex / DNA strand resection involved in replication fork processing / chordate embryonic development / negative regulation of fatty acid biosynthetic process / cellular response to indole-3-methanol / homologous recombination / lateral element / XY body / protein K6-linked ubiquitination / regulation of DNA damage checkpoint / dosage compensation by inactivation of X chromosome / negative regulation of gene expression via chromosomal CpG island methylation / Impaired BRCA2 binding to PALB2 / 5'-3' DNA helicase activity / : / mitotic G2/M transition checkpoint / postreplication repair / cellular response to angiotensin / DNA repair complex / RNA polymerase binding / centrosome cycle / 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) / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / intracellular non-membrane-bounded organelle / response to ionizing radiation / DNA-binding transcription activator activity / seminiferous tubule development / Transcriptional Regulation by E2F6 / spermatid development / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / negative regulation of cell cycle / positive regulation of vascular endothelial growth factor production / negative regulation of reactive oxygen species metabolic process / localization / regulation of DNA repair / protein autoubiquitination / SUMOylation of DNA damage response and repair proteins / ubiquitin ligase complex / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of DNA repair / DNA helicase activity / Meiotic synapsis / tubulin binding / DNA damage checkpoint signaling / male germ cell nucleus / chromosome segregation / cellular response to ionizing radiation / nucleotide-excision repair / TP53 Regulates Transcription of DNA Repair Genes / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / HDR through Homologous Recombination (HRR) / response to toxic substance / G2/M DNA damage checkpoint / Metalloprotease DUBs / Meiotic recombination / negative regulation of cell growth / protein polyubiquitination / ubiquitin-protein transferase activity / fatty acid biosynthetic process / positive regulation of angiogenesis / KEAP1-NFE2L2 pathway / intrinsic apoptotic signaling pathway in response to DNA damage / double-strand break repair / p53 binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Neddylation / chromosome / 4 iron, 4 sulfur cluster binding / Processing of DNA double-strand break ends / cellular response to tumor necrosis factor / cellular response to hypoxia / nuclear membrane / Regulation of TP53 Activity through Phosphorylation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Shiozaki, E.N. / Gu, L. / Yan, N. / Shi, Y. | ||||||
Citation | Journal: Mol.Cell / Year: 2004 Title: Structure of the BRCT repeats of BRCA1 bound to a BACH1 phosphopeptide: implications for signaling. Authors: Shiozaki, E.N. / Gu, L. / Yan, N. / Shi, Y. | ||||||
History |
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Remark 999 | SEQUENCE Residue THR 1816 and residue GLU 1817 chain A are not linked. Distance of C-N bond is 3.29A. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t29.cif.gz | 63.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t29.ent.gz | 45.6 KB | Display | PDB format |
PDBx/mmJSON format | 1t29.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t2/1t29 ftp://data.pdbj.org/pub/pdb/validation_reports/t2/1t29 | HTTPS FTP |
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-Related structure data
Related structure data | 1jnxS 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: 24531.234 Da / Num. of mol.: 1 / Fragment: BRCT repeats of BRCA1 (residues 1646-1859) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38398 |
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#2: Protein/peptide | Mass: 1677.770 Da / Num. of mol.: 1 / Fragment: residues 985-998 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide occurs naturally in humans References: UniProt: Q9BX63 |
#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: 2.43 Å3/Da / Density % sol: 48.9 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 30, 2004 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→99 Å / Num. all: 11334 / Num. obs: 11209 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 40 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 |
Reflection shell | Resolution: 2.3→2.4 Å / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 0.179 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1JNX Resolution: 2.3→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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Xplor file |
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