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Yorodumi- PDB-3pxa: Impact of BRCA1 BRCT domain missense substitutions on phospho-pep... -
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-Basic information
Entry | Database: PDB / ID: 3pxa | ||||||
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Title | Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: G1656D | ||||||
Components | Breast cancer type 1 susceptibility protein | ||||||
Keywords | PROTEIN BINDING / BRCA1 protein / Missense / phosphopeptide recognition / BRCT tandem repeats / Bach1 Ctip Abraxas / Nuclear Protein | ||||||
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 / sex-chromosome dosage compensation / negative regulation of intracellular estrogen receptor signaling pathway ...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 / sex-chromosome dosage compensation / negative regulation of intracellular estrogen receptor signaling pathway / gamma-tubulin ring complex / nuclear ubiquitin ligase complex / chordate embryonic development / cellular response to indole-3-methanol / negative regulation of fatty acid biosynthetic process / lateral element / homologous recombination / DNA strand resection involved in replication fork processing / protein K6-linked ubiquitination / regulation of DNA damage checkpoint / Impaired BRCA2 binding to PALB2 / XY body / 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 / intracellular non-membrane-bounded organelle / HDR through Single Strand Annealing (SSA) / negative regulation of gene expression via chromosomal CpG island methylation / Impaired BRCA2 binding to RAD51 / DNA-binding transcription activator activity / response to ionizing radiation / 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 / positive regulation of DNA repair / protein autoubiquitination / male germ cell nucleus / SUMOylation of DNA damage response and repair proteins / regulation of DNA repair / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ubiquitin ligase complex / Meiotic synapsis / tubulin binding / Meiotic recombination / Nonhomologous End-Joining (NHEJ) / chromosome segregation / cellular response to ionizing radiation / TP53 Regulates Transcription of DNA Repair Genes / G2/M DNA damage checkpoint / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / HDR through Homologous Recombination (HRR) / negative regulation of cell growth / p53 binding / Metalloprotease DUBs / fatty acid biosynthetic process / positive regulation of angiogenesis / ubiquitin-protein transferase activity / chromosome / intrinsic apoptotic signaling pathway in response to DNA damage / KEAP1-NFE2L2 pathway / double-strand break repair / Processing of DNA double-strand break ends / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to tumor necrosis factor / Neddylation / Regulation of TP53 Activity through Phosphorylation / transcription coactivator activity / transcription cis-regulatory region binding / damaged DNA binding / nuclear body / regulation of cell cycle / protein ubiquitination / ribonucleoprotein complex / DNA repair / negative regulation of DNA-templated transcription / DNA damage response / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / positive regulation of gene expression / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Coquelle, N. / Green, R. / Glover, J.N.M. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Impact of BRCA1 BRCT Domain Missense Substitutions on Phosphopeptide Recognition. Authors: Coquelle, N. / Green, R. / Glover, J.N. #1: Journal: Cancer Res. / Year: 2010 Title: Comprehensive analysis of missense variations in the BRCT domain of BRCA1 by structural and functional assays. Authors: Lee, M.S. / Green, R. / Marsillac, S.M. / Coquelle, N. / Williams, R.S. / Yeung, T. / Foo, D. / Hau, D.D. / Hui, B. / Monteiro, A.N. / Glover, J.N. #2: Journal: Nat.Struct.Mol.Biol. / Year: 2004 Title: Structural basis of phosphopeptide recognition by the BRCT domain of BRCA1. Authors: Williams, R.S. / Lee, M.S. / Hau, D.D. / Glover, J.N. #3: Journal: Nat.Struct.Mol.Biol. / Year: 2004 Title: Structure and mechanism of BRCA1 BRCT domain recognition of phosphorylated BACH1 with implications for cancer. Authors: Clapperton, J.A. / Manke, I.A. / Lowery, D.M. / Ho, T. / Haire, L.F. / Yaffe, M.B. / Smerdon, S.J. #4: Journal: J.Biol.Chem. / Year: 2003 Title: Structural consequences of a cancer-causing BRCA1-BRCT missense mutation. Authors: Williams, R.S. / Glover, J.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pxa.cif.gz | 101 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pxa.ent.gz | 77.2 KB | Display | PDB format |
PDBx/mmJSON format | 3pxa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pxa_validation.pdf.gz | 435.9 KB | Display | wwPDB validaton report |
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Full document | 3pxa_full_validation.pdf.gz | 438.3 KB | Display | |
Data in XML | 3pxa_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 3pxa_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/px/3pxa ftp://data.pdbj.org/pub/pdb/validation_reports/px/3pxa | HTTPS FTP |
-Related structure data
Related structure data | 3pxbC 3pxcC 3pxdC 3pxeC 1n5oS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 24589.271 Da / Num. of mol.: 1 / Fragment: BRCT Domain, UNP residues 1646-1859 / Mutation: G1656D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRCA1, RNF53 / Plasmid: pLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold References: UniProt: P38398, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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#2: Chemical | ChemComp-NI / |
#3: Chemical | ChemComp-SO4 / |
#4: 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: 4.73 Å3/Da / Density % sol: 73.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.0M Li2SO4 100mM Tris 5mM CaCl2 10mM NiCl2 , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å | |||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 11, 2009 | |||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.55→40 Å / Num. all: 15761 / Num. obs: 15761 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 65 Å2 / Rsym value: 0.051 / Net I/σ(I): 18.4 | |||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1N5O Resolution: 2.55→37.672 Å / SU ML: 0.35 / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.589 Å2 / ksol: 0.342 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.55→37.672 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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