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Yorodumi- PDB-1jnx: Crystal structure of the BRCT repeat region from the breast cance... -
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-Basic information
Entry | Database: PDB / ID: 1jnx | ||||||
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Title | Crystal structure of the BRCT repeat region from the breast cancer associated protein, BRCA1 | ||||||
Components | BREAST CANCER TYPE 1 SUSCEPTIBILITY PROTEIN | ||||||
Keywords | GENE REGULATION / BRCT / CANCER / GENE EXPRESSION | ||||||
Function / homology | Function and homology information Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function / : / BRCA1-BARD1 complex / : / BRCA1-C complex / BRCA1-B complex / BRCA1-A complex / random inactivation of X chromosome / negative regulation of centriole replication ...Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function / : / 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 / 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 / : / mitotic G2/M transition checkpoint / postreplication repair / 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 / Transcriptional Regulation by E2F6 / 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 / Meiotic synapsis / tubulin binding / male germ cell nucleus / chromosome segregation / cellular response to ionizing radiation / 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) / 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 / Processing of DNA double-strand break ends / cellular response to tumor necrosis factor / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / transcription coactivator activity / nuclear body / transcription cis-regulatory region binding / protein ubiquitination / regulation of cell cycle / ribonucleoprotein complex / DNA repair / negative regulation of DNA-templated transcription / DNA damage response / ubiquitin protein ligase binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Williams, R.S. / Green, R. / Glover, J.N.M. | ||||||
Citation | Journal: Nat Struct Biol / Year: 2001 Title: Crystal structure of the BRCT repeat region from the breast cancer-associated protein BRCA1. Authors: R S Williams / R Green / J N Glover / Abstract: The C-terminal BRCT region of BRCA1 is essential for its DNA repair, transcriptional regulation and tumor suppressor functions. Here we determine the crystal structure of the BRCT domain of human ...The C-terminal BRCT region of BRCA1 is essential for its DNA repair, transcriptional regulation and tumor suppressor functions. Here we determine the crystal structure of the BRCT domain of human BRCA1 at 2.5 A resolution. The domain contains two BRCT repeats that adopt similar structures and are packed together in a head-to-tail arrangement. Cancer-causing missense mutations occur at the interface between the two repeats and destabilize the structure. The manner by which the two BRCT repeats interact in BRCA1 may represent a general mode of interaction between homologous domains within proteins that interact to regulate the cellular response to DNA damage. The structure provides a basis to predict the structural consequences of uncharacterized BRCA1 mutations. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jnx.cif.gz | 55.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jnx.ent.gz | 39.1 KB | Display | PDB format |
PDBx/mmJSON format | 1jnx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jn/1jnx ftp://data.pdbj.org/pub/pdb/validation_reports/jn/1jnx | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: residues 1646-1859 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRCA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P38398 |
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#2: Chemical | ChemComp-NI / |
#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: 4.74 Å3/Da / Density % sol: 74.03 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / pH: 8.5 Details: Lithium sulphate, Nickel sulphate, calcium chloride, Tris, pH 8.5,VAPOR DIFFUSION, HANGING DROP at 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20-23 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 4, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40 Å / Num. obs: 16968 / % possible obs: 99.8 % / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.5→2.57 Å / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. measured all: 209566 / Rmerge(I) obs: 0.048 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 9.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: TLS PARAMETERS FOR REFMAC: GROUP- CHAIN X,N,&W, ALL ATOMS: T TENSOR: T11: 0.3885 T22: 0.2528 T33: 0.0541 T12: 0.2422 T13: -0.0261 T23: 0.0567 L TENSOR: L11: 15.0684 L22: 14.6911 L33: 2.1404 ...Details: TLS PARAMETERS FOR REFMAC: GROUP- CHAIN X,N,&W, ALL ATOMS: T TENSOR: T11: 0.3885 T22: 0.2528 T33: 0.0541 T12: 0.2422 T13: -0.0261 T23: 0.0567 L TENSOR: L11: 15.0684 L22: 14.6911 L33: 2.1404 L12: -13.6906 L13: 4.0117 L23: -2.8964 S TENSOR: S11: 1.1964 S12: 1.4251 S13: 0.4307 S21: -1.4475 S22: -1.3203 S23: -0.2414 S31: 0.2422 S32: 0.5625 S33: 0.1239
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Refinement step | Cycle: LAST / Resolution: 2.5→25 Å
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Refinement TLS params. | Method: refined / Origin x: 24.4147 Å / Origin y: 58.8128 Å / Origin z: 37.1148 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 5.1 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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