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Yorodumi- PDB-4cri: Crystal Structure of 53BP1 tandem tudor domains in complex with m... -
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-Basic information
Entry | Database: PDB / ID: 4cri | ||||||
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Title | Crystal Structure of 53BP1 tandem tudor domains in complex with methylated K810 Rb peptide | ||||||
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Keywords | PEPTIDE BINDING PROTEIN / TUMOUR SUPPRESSOR PRB / 53BP1 | ||||||
Function / homology | Function and homology information Defective translocation of RB1 mutants to the nucleus / enucleate erythrocyte differentiation / positive regulation of collagen fibril organization / negative regulation of tau-protein kinase activity / Rb-E2F complex / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / regulation of lipid kinase activity / negative regulation of myofibroblast differentiation / maintenance of mitotic sister chromatid cohesion / cell morphogenesis involved in neuron differentiation ...Defective translocation of RB1 mutants to the nucleus / enucleate erythrocyte differentiation / positive regulation of collagen fibril organization / negative regulation of tau-protein kinase activity / Rb-E2F complex / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / regulation of lipid kinase activity / negative regulation of myofibroblast differentiation / maintenance of mitotic sister chromatid cohesion / cell morphogenesis involved in neuron differentiation / chromatin lock complex / sister chromatid biorientation / ubiquitin-modified histone reader activity / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / positive regulation of extracellular matrix organization / positive regulation of isotype switching / regulation of centromere complex assembly / Aberrant regulation of mitotic exit in cancer due to RB1 defects / positive regulation of macrophage differentiation / positive regulation of transcription regulatory region DNA binding / cellular response to X-ray / glial cell apoptotic process / tissue homeostasis / protein localization to chromosome, centromeric region / negative regulation of protein serine/threonine kinase activity / positive regulation of mitotic metaphase/anaphase transition / importin-alpha family protein binding / negative regulation of hepatocyte apoptotic process / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / neuron maturation / digestive tract development / aortic valve morphogenesis / DNA repair complex / Replication of the SARS-CoV-1 genome / myoblast differentiation / negative regulation of cold-induced thermogenesis / SWI/SNF complex / Cyclin E associated events during G1/S transition / negative regulation of glial cell proliferation / smoothened signaling pathway / negative regulation of G1/S transition of mitotic cell cycle / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / telomeric DNA binding / histone reader activity / hepatocyte apoptotic process / Cyclin A:Cdk2-associated events at S phase entry / skeletal muscle cell differentiation / RUNX2 regulates osteoblast differentiation / regulation of mitotic cell cycle / transcription factor binding / SUMOylation of transcription factors / negative regulation of apoptotic signaling pathway / negative regulation of cell cycle / chromosome organization / glial cell proliferation / chondrocyte differentiation / negative regulation of double-strand break repair via homologous recombination / Nuclear events stimulated by ALK signaling in cancer / negative regulation of smoothened signaling pathway / transcription coregulator activity / epithelial cell proliferation / striated muscle cell differentiation / methylated histone binding / Condensation of Prophase Chromosomes / DNA damage checkpoint signaling / replication fork / Nonhomologous End-Joining (NHEJ) / phosphoprotein binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / kinase binding / negative regulation of protein kinase activity / positive regulation of DNA-binding transcription factor activity / G2/M DNA damage checkpoint / negative regulation of inflammatory response / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / protein homooligomerization / Cyclin D associated events in G1 / negative regulation of DNA-binding transcription factor activity / Oncogene Induced Senescence / G1/S transition of mitotic cell cycle / cellular response to insulin stimulus / heterochromatin formation / PML body / negative regulation of cell growth / p53 binding / kinetochore / spindle / double-strand break repair via nonhomologous end joining / cellular response to xenobiotic stimulus / transcription corepressor activity / negative regulation of epithelial cell proliferation / disordered domain specific binding / neuron projection development / Processing of DNA double-strand break ends / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / Replication of the SARS-CoV-2 genome / histone binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Krojer, T. / Johansson, C. / Gileadi, C. / Fedorov, O. / Carr, S. / La Thangue, N.B. / Vollmar, M. / Crawley, L. / von Delft, F. / Bountra, C. ...Krojer, T. / Johansson, C. / Gileadi, C. / Fedorov, O. / Carr, S. / La Thangue, N.B. / Vollmar, M. / Crawley, L. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Oppermann, U. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Lysine Methylation-Dependent Binding of 53BP1 to the Prb Tumor Suppressor. Authors: Carr, S.M. / Munro, S. / Zalmas, L. / Fedorov, O. / Johansson, C. / Krojer, T. / Sagum, C.A. / Bedford, M.T. / Oppermann, U. / La Thangue, N.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cri.cif.gz | 116.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cri.ent.gz | 91.6 KB | Display | PDB format |
PDBx/mmJSON format | 4cri.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cri_validation.pdf.gz | 454 KB | Display | wwPDB validaton report |
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Full document | 4cri_full_validation.pdf.gz | 457.1 KB | Display | |
Data in XML | 4cri_validation.xml.gz | 12 KB | Display | |
Data in CIF | 4cri_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cr/4cri ftp://data.pdbj.org/pub/pdb/validation_reports/cr/4cri | HTTPS FTP |
-Related structure data
Related structure data | 3lh0S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 19447.787 Da / Num. of mol.: 2 / Fragment: TANDEM TUDOR DOMAIN, RESIDUES 1459-1634 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q12888 #2: Protein/peptide | Mass: 1941.274 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P78495, UniProt: P06400*PLUS #3: 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: 2.43 Å3/Da / Density % sol: 58.28 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 5%(W/V) PEG10K. 0.15M MAGNESIUM CHLORIDE, 0.1M TRIS PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→52.05 Å / Num. obs: 22195 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Biso Wilson estimate: 59.65 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2.2 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3LH0 Resolution: 2.35→39.51 Å / SU ML: 0.32 / σ(F): 1.35 / Phase error: 25.27 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→39.51 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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