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Yorodumi- PDB-8u4u: Crystal structure of 53BP1 tandem Tudor domain homodimer engineer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8u4u | ||||||||||||
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Title | Crystal structure of 53BP1 tandem Tudor domain homodimer engineered with two disulfide bridges | ||||||||||||
Components | TP53-binding protein 1 | ||||||||||||
Keywords | SIGNALING PROTEIN / 53BP1 / DNA damage response / DNA double-strand break repair / non-homologous end joining / homologous recombination / chromatin-binding protein / engineered protein | ||||||||||||
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 / DNA repair complex / telomeric DNA binding / SUMOylation of transcription factors / negative regulation of double-strand break repair via homologous recombination / methylated histone binding ...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 / DNA repair complex / telomeric DNA binding / SUMOylation of transcription factors / negative regulation of double-strand break repair via homologous recombination / methylated histone binding / histone reader activity / replication fork / DNA damage checkpoint signaling / Nonhomologous End-Joining (NHEJ) / transcription coregulator activity / G2/M DNA damage checkpoint / protein homooligomerization / kinetochore / positive regulation of DNA-binding transcription factor activity / double-strand break repair via nonhomologous end joining / p53 binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / Processing of DNA double-strand break ends / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / chromosome, telomeric region / damaged DNA binding / nuclear body / DNA damage response / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.79 Å | ||||||||||||
Authors | Cui, G. / Botuyan, M.V. / Thompson, J.R. / Mer, G. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat Commun / Year: 2023 Title: An autoinhibited state of 53BP1 revealed by small molecule antagonists and protein engineering. Authors: Cui, G. / Botuyan, M.V. / Drane, P. / Hu, Q. / Bragantini, B. / Thompson, J.R. / Schuller, D.J. / Detappe, A. / Perfetti, M.T. / James, L.I. / Frye, S.V. / Chowdhury, D. / Mer, G. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8u4u.cif.gz | 763.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8u4u.ent.gz | 593.7 KB | Display | PDB format |
PDBx/mmJSON format | 8u4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8u4u_validation.pdf.gz | 501.3 KB | Display | wwPDB validaton report |
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Full document | 8u4u_full_validation.pdf.gz | 512.9 KB | Display | |
Data in XML | 8u4u_validation.xml.gz | 40.5 KB | Display | |
Data in CIF | 8u4u_validation.cif.gz | 53.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/8u4u ftp://data.pdbj.org/pub/pdb/validation_reports/u4/8u4u | HTTPS FTP |
-Related structure data
Related structure data | 6mxxC 6mxyC 6mxzC 6my0C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 14047.006 Da / Num. of mol.: 10 / Mutation: E1549C, E1567C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TP53BP1 / Plasmid: pHISPP / Production host: Escherichia coli (E. coli) / References: UniProt: Q12888 |
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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: 3.76 Å3/Da / Density % sol: 67.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Crystals of the protein (15 mg/mL) were obtained by the hanging drop vapor diffusion method, mixing 1 microliter of the sample in 50 mM Tris-HCl, pH 7.0, 100 mM NaCl and 1 microliter of the ...Details: Crystals of the protein (15 mg/mL) were obtained by the hanging drop vapor diffusion method, mixing 1 microliter of the sample in 50 mM Tris-HCl, pH 7.0, 100 mM NaCl and 1 microliter of the reservoir solution (0.1 M Bis-Tris, pH 6.5) at 293 K. The crystals were cryoprotected with 25% (w/v) xylitol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 3.79→50 Å / Num. obs: 19541 / % possible obs: 89.41 % / Redundancy: 5.7 % / Biso Wilson estimate: 109.86 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1197 / Rpim(I) all: 0.05194 / Rrim(I) all: 0.1311 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 3.79→3.926 Å / Rmerge(I) obs: 0.6143 / Mean I/σ(I) obs: 3.23 / Num. unique obs: 1631 / CC1/2: 0.813 / Rpim(I) all: 0.2842 / Rrim(I) all: 0.6804 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.79→48.19 Å / SU ML: 0.5358 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.3893 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 142.67 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.79→48.19 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 | Refine-ID: X-RAY DIFFRACTION
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