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Yorodumi- PDB-5kgf: Structural model of 53BP1 bound to a ubiquitylated and methylated... -
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-Basic information
Entry | Database: PDB / ID: 5kgf | ||||||||||||
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Title | Structural model of 53BP1 bound to a ubiquitylated and methylated nucleosome, at 4.5 A resolution | ||||||||||||
Components |
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Keywords | STRUCTURAL PROTEIN/DNA / DNA / chromatin / 53BP1 / STRUCTURAL PROTEIN-DNA complex | ||||||||||||
Function / homology | Function and homology information ubiquitin-modified histone reader activity / intracellular organelle / 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 / hypothalamus gonadotrophin-releasing hormone neuron development / DNA repair complex / female meiosis I / positive regulation of protein monoubiquitination ...ubiquitin-modified histone reader activity / intracellular organelle / 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 / hypothalamus gonadotrophin-releasing hormone neuron development / DNA repair complex / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / telomeric DNA binding / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / SUMOylation of transcription factors / negative regulation of double-strand break repair via homologous recombination / regulation of neuron apoptotic process / Replacement of protamines by nucleosomes in the male pronucleus / regulation of proteasomal protein catabolic process / Packaging Of Telomere Ends / energy homeostasis / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Maturation of protein E / Deposition of new CENPA-containing nucleosomes at the centromere / Maturation of protein E / ER Quality Control Compartment (ERQC) / nucleosomal DNA binding / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / methylated histone binding / Prevention of phagosomal-lysosomal fusion / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Inhibition of DNA recombination at telomere / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / TICAM1,TRAF6-dependent induction of TAK1 complex / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of FZD by ubiquitination / TICAM1-dependent activation of IRF3/IRF7 / histone reader activity / NOTCH2 Activation and Transmission of Signal to the Nucleus / p75NTR recruits signalling complexes / APC/C:Cdc20 mediated degradation of Cyclin B / VLDLR internalisation and degradation / Meiotic synapsis / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / RNA Polymerase I Promoter Opening / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / Assembly of the ORC complex at the origin of replication / NRIF signals cell death from the nucleus / Pexophagy / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of PTEN localization / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / DNA methylation / Translesion synthesis by POLK / neuron projection morphogenesis / Condensation of Prophase Chromosomes / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Gap-filling DNA repair synthesis and ligation in GG-NER / regulation of mitochondrial membrane potential / SIRT1 negatively regulates rRNA expression / Josephin domain DUBs / InlB-mediated entry of Listeria monocytogenes into host cell / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PINK1-PRKN Mediated Mitophagy / DNA damage checkpoint signaling Similarity search - Function | ||||||||||||
Biological species | Xenopus laevis (African clawed frog) Homo sapiens (human) synthetic construct (others) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.54 Å | ||||||||||||
Authors | Wilson, M.D. / Benlekbir, S. / Sicheri, F. / Rubinstein, J.L. / Durocher, D. | ||||||||||||
Funding support | Canada, 3items
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Citation | Journal: Nature / Year: 2016 Title: The structural basis of modified nucleosome recognition by 53BP1. Abstract: DNA double-strand breaks (DSBs) elicit a histone modification cascade that controls DNA repair. This pathway involves the sequential ubiquitination of histones H1 and H2A by the E3 ubiquitin ligases ...DNA double-strand breaks (DSBs) elicit a histone modification cascade that controls DNA repair. This pathway involves the sequential ubiquitination of histones H1 and H2A by the E3 ubiquitin ligases RNF8 and RNF168, respectively. RNF168 ubiquitinates H2A on lysine 13 and lysine 15 (refs 7, 8) (yielding H2AK13ub and H2AK15ub, respectively), an event that triggers the recruitment of 53BP1 (also known as TP53BP1) to chromatin flanking DSBs. 53BP1 binds specifically to H2AK15ub-containing nucleosomes through a peptide segment termed the ubiquitination-dependent recruitment motif (UDR), which requires the simultaneous engagement of histone H4 lysine 20 dimethylation (H4K20me2) by its tandem Tudor domain. How 53BP1 interacts with these two histone marks in the nucleosomal context, how it recognizes ubiquitin, and how it discriminates between H2AK13ub and H2AK15ub is unknown. Here we present the electron cryomicroscopy (cryo-EM) structure of a dimerized human 53BP1 fragment bound to a H4K20me2-containing and H2AK15ub-containing nucleosome core particle (NCP-ubme) at 4.5 Å resolution. The structure reveals that H4K20me2 and H2AK15ub recognition involves intimate contacts with multiple nucleosomal elements including the acidic patch. Ubiquitin recognition by 53BP1 is unusual and involves the sandwiching of the UDR segment between ubiquitin and the NCP surface. The selectivity for H2AK15ub is imparted by two arginine fingers in the H2A amino-terminal tail, which straddle the nucleosomal DNA and serve to position ubiquitin over the NCP-bound UDR segment. The structure of the complex between NCP-ubme and 53BP1 reveals the basis of 53BP1 recruitment to DSB sites and illuminates how combinations of histone marks and nucleosomal elements cooperate to produce highly specific chromatin responses, such as those elicited following chromosome breaks. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5kgf.cif.gz | 358.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kgf.ent.gz | 279.5 KB | Display | PDB format |
PDBx/mmJSON format | 5kgf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kgf_validation.pdf.gz | 981.4 KB | Display | wwPDB validaton report |
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Full document | 5kgf_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5kgf_validation.xml.gz | 47.9 KB | Display | |
Data in CIF | 5kgf_validation.cif.gz | 72.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/5kgf ftp://data.pdbj.org/pub/pdb/validation_reports/kg/5kgf | HTTPS FTP |
-Related structure data
Related structure data | 8246MC 8247C M: map data used to model this data 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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-Components
-Protein , 5 types, 10 molecules AEBFCGDHOM
#1: Protein | Mass: 15421.101 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233 #2: Protein | Mass: 11439.511 Da / Num. of mol.: 2 / Mutation: K20C Source method: isolated from a genetically manipulated source Details: cysteine alkylation at position 20 / Source: (gene. exp.) Xenopus laevis (African clawed frog) / Details (production host): pDD2349 / Production host: Escherichia coli (E. coli) / References: UniProt: P62799 #3: Protein | Mass: 14163.539 Da / Num. of mol.: 2 / Mutation: K13R, T16S, K36R Source method: isolated from a genetically manipulated source Details: Isopeptide amide crosslink between K15 of H2A and G76 of ubiquitin Source: (gene. exp.) Homo sapiens (human) Gene: HIST1H2AG, H2AFP, HIST1H2AI, H2AFC, HIST1H2AK, H2AFD, HIST1H2AL, H2AFI, HIST1H2AM, H2AFN Production host: Escherichia coli (E. coli) / References: UniProt: P0C0S8 #4: Protein | Mass: 13937.213 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: HIST1H2BC, H2BFL, HIST1H2BE, H2BFH, HIST1H2BF, H2BFG, HIST1H2BG, H2BFA, HIST1H2BI, H2BFK Production host: Escherichia coli (E. coli) / References: UniProt: P62807 #8: Protein | Mass: 8576.831 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47 |
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-DNA chain , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 44520.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
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#6: DNA chain | Mass: 44991.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
-Protein/peptide , 1 types, 2 molecules LK
#7: Protein/peptide | Mass: 2376.757 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: full protein not modeled / Source: (gene. exp.) Homo sapiens (human) / Gene: TP53BP1 / Production host: Escherichia coli (E. coli) / References: UniProt: H7BZY0, UniProt: Q12888*PLUS |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 Details: High concentration NCP-ubme/GST-53BP1 complex at 200 mM salt was diluted just prior to grid freezing. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER/RHODIUM / Grid mesh size: 400 divisions/in. / Grid type: electron micrsocopy sciences | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K Details: Plunged into liquid ethane-propane (FEI VITROBOT MARK III) |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 25000 X / Calibrated magnification: 34483 X / Cs: 2 mm / C2 aperture diameter: 30 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER |
Image recording | Average exposure time: 0.5 sec. / Electron dose: 36 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 319 |
Image scans | Movie frames/image: 30 / Used frames/image: 1-30 |
-Processing
Software | Name: PHENIX / Version: 1.10.1_2155: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 174185 Details: Automatically picked from roughly 3000 particles using a manually picked template | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45361 / Algorithm: FOURIER SPACE / Num. of class averages: 9 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 207.5 / Protocol: RIGID BODY FIT / Space: REAL Details: The atomic models of Widom-601 DNA (PDB ID 3LZ0), octameric histones (PDB ID 1KX5), ubiquitin (PDB ID 1UBI), and H4K20me2/53BP1 tandem Tudor domain (PDB ID 2IG0) were fitted without allowing ...Details: The atomic models of Widom-601 DNA (PDB ID 3LZ0), octameric histones (PDB ID 1KX5), ubiquitin (PDB ID 1UBI), and H4K20me2/53BP1 tandem Tudor domain (PDB ID 2IG0) were fitted without allowing flexibility into the 3D maps using UCSF Chimera. Segmentation was performed in UCSF Chimera. For the NCP-ubme structure the ubiquitin segmentation was further modified to remove obvious NCP density from the ubiquitin segment. The H2A/H2B sequence was mutated to the human H2AK13R/K36R and H2B manually in UCSF Chimera. A polyalanine model of the UDR was built within the UDR density in Coot, which compared well to predicted structures generated by Rosetta. The UDR model was mutated and fitted using UCSF Chimera, followed by iterative rounds of real-space refinement in PHENIX and model optimization in Coot. All figures were prepared in UCSF Chimera. | ||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 4.54 Å | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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