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Yorodumi- PDB-1gzh: Crystal structure of the BRCT domains of human 53BP1 bound to the... -
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-Basic information
Entry | Database: PDB / ID: 1gzh | ||||||
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Title | Crystal structure of the BRCT domains of human 53BP1 bound to the p53 tumor supressor | ||||||
Components |
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Keywords | GENE REGULATION / ANTI-ONCOGENE / DNA-BINDING / TRANSCRIPTION REGULATION / BCRT DOMAIN / APOPTOSIS / DISEASE MUTATION / ACTIVATOR / DNA- REPAIR | ||||||
Function / homology | Function and homology information ubiquitin-modified histone reader activity / positive regulation of isotype switching / cellular response to X-ray / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate ...ubiquitin-modified histone reader activity / positive regulation of isotype switching / cellular response to X-ray / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / glucose catabolic process to lactate via pyruvate / regulation of tissue remodeling / DNA repair complex / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / histone deacetylase regulator activity / germ cell nucleus / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / regulation of DNA damage response, signal transduction by p53 class mediator / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of glial cell proliferation / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / mitochondrial DNA repair / T cell lineage commitment / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / telomeric DNA binding / histone reader activity / ER overload response / negative regulation of DNA replication / B cell lineage commitment / positive regulation of cardiac muscle cell apoptotic process / thymocyte apoptotic process / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TP53 Regulates Transcription of Caspase Activators and Caspases / mitotic G1 DNA damage checkpoint signaling / cardiac septum morphogenesis / positive regulation of execution phase of apoptosis / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / Zygotic genome activation (ZGA) / necroptotic process / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / rRNA transcription / TFIID-class transcription factor complex binding / negative regulation of telomere maintenance via telomerase / SUMOylation of transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / general transcription initiation factor binding / mitophagy / Transcriptional Regulation by VENTX / DNA damage response, signal transduction by p53 class mediator / response to X-ray / replicative senescence / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to UV-C / neuroblast proliferation / : / negative regulation of reactive oxygen species metabolic process / hematopoietic stem cell differentiation / chromosome organization / positive regulation of RNA polymerase II transcription preinitiation complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / T cell proliferation involved in immune response / glial cell proliferation / Pyroptosis / cis-regulatory region sequence-specific DNA binding / negative regulation of double-strand break repair via homologous recombination / embryonic organ development / hematopoietic progenitor cell differentiation / cellular response to actinomycin D / somitogenesis / type II interferon-mediated signaling pathway / cellular response to glucose starvation / core promoter sequence-specific DNA binding / negative regulation of stem cell proliferation Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Derbyshire, D.J. / Doherty, A.J. | ||||||
Citation | Journal: Embo J. / Year: 2002 Title: Crystal Structure of Human 53BP1 Brct Domains Bound to P53 Tumour Suppressor Authors: Derbyshire, D.J. / Basu, B.P. / Serpell, L. / Joo, W. / Date, T. / Iwabuchi, K. / Doherty, A.J. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Purification, Crystallization and Preliminary X-Ray Analysis of the Brct Domains of Human 53BP1 Bound to the P53 Tumour Suppressor. Authors: Derbyshire, D.J. / Basu, B.P. / Date, T. / Iwabuchi, K. / Doherty, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gzh.cif.gz | 176.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gzh.ent.gz | 138.1 KB | Display | PDB format |
PDBx/mmJSON format | 1gzh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gzh_validation.pdf.gz | 471 KB | Display | wwPDB validaton report |
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Full document | 1gzh_full_validation.pdf.gz | 491.1 KB | Display | |
Data in XML | 1gzh_validation.xml.gz | 32.7 KB | Display | |
Data in CIF | 1gzh_validation.cif.gz | 44.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/1gzh ftp://data.pdbj.org/pub/pdb/validation_reports/gz/1gzh | HTTPS FTP |
-Related structure data
Related structure data | 1tsrS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-CELLULAR TUMOR ANTIGEN ... , 2 types, 2 molecules AC
#1: Protein | Mass: 22375.479 Da / Num. of mol.: 1 / Fragment: DNA BINDING REGION, RESIDUES 95-292 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PRSET-B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3)PLYSS / References: UniProt: P04637 |
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#3: Protein | Mass: 22361.453 Da / Num. of mol.: 1 / Fragment: DNA BINDING REGION, RESIDUES 95-292 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PRSET-B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3)PLYSS / References: UniProt: P04637 |
-Protein , 1 types, 2 molecules BD
#2: Protein | Mass: 28175.900 Da / Num. of mol.: 2 / Fragment: BRCT TANDEM REPEAT, RESIDUES 1724-1972 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PRSET-A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3)PLYSS / References: UniProt: Q12888 |
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-Non-polymers , 3 types, 114 molecules
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 41.76 % Description: STRUCTURE DETERMINATION COMPLETED BY MOLECULAR REPLACEMENT WITH PDB ENTRY 1KZY (VIA PERSONAL COMMUNICATION) | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.4 Details: 50 MM TRIS PH 7.4, 250 MM AMMONIUM SULFATE, 25% POLYETHYLENE GLYCOL 4000 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→38.84 Å / Num. obs: 54119 / % possible obs: 99.1 % / Redundancy: 7.7 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 1.4 / % possible all: 96.9 |
Reflection | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 55 Å |
Reflection shell | *PLUS % possible obs: 96.9 % / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TSR Resolution: 2.6→38.84 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1861614.03 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: CHAIN A HAS BREAKS BETWEEN RESIDUES 183-188 AND 224-227. DISORDER IS ALSO EVIDENT FOR RESIDUE 200. CHAIN B IS UNINTREPRETABLE BETWEEN RESIDUES 1750-1768. CHAIN C HAS NO BREAKS BUT ONLY ...Details: CHAIN A HAS BREAKS BETWEEN RESIDUES 183-188 AND 224-227. DISORDER IS ALSO EVIDENT FOR RESIDUE 200. CHAIN B IS UNINTREPRETABLE BETWEEN RESIDUES 1750-1768. CHAIN C HAS NO BREAKS BUT ONLY EXTENDS FROM 95-289. CHAIN D HAS A BREAK BETWEEN 1740-1768 AND 1794-1796, AND ONLY EXTENDS FROM 1725-1969.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 18.1016 Å2 / ksol: 0.340415 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→38.84 Å
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Refine LS restraints |
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Refine LS restraints NCS | Rms dev Biso : 15 Å2 / Rms dev position: 1.99 Å / Weight Biso : 2 / Weight position: 300 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.62 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 50
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 500 Å / % reflection Rfree: 5.2 % / Rfactor Rfree: 0.2883 / Rfactor Rwork: 0.2381 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.34 |