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Yorodumi- EMDB-34028: cryo-EM structure of gammaH2AXK15ub-H4K20me2 nucleosome bound to 53BP1 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34028 | ||||||||||||||||||
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Title | cryo-EM structure of gammaH2AXK15ub-H4K20me2 nucleosome bound to 53BP1 | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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Keywords | nucleosoeme / 53BP1 / complex / H4K20me2 / H2AXK15ub / gammaH2AX / NUCLEAR PROTEIN | ||||||||||||||||||
Function / homology | Function and homology information Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression ...Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / DNA damage checkpoint signaling / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / modification-dependent protein catabolic process / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / protein tag activity / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / nuclear body / protein ubiquitination / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / ubiquitin protein ligase binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.38 Å | ||||||||||||||||||
Authors | Ai HS / GuoChao C / Qingyue G / Ze-Bin T / Zhiheng D / Xin L / Fan Y / Ziyu X / Jia-Bin L / Changlin T / Liu L | ||||||||||||||||||
Funding support | China, 5 items
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Citation | Journal: J Am Chem Soc / Year: 2022 Title: Chemical Synthesis of Post-Translationally Modified H2AX Reveals Redundancy in Interplay between Histone Phosphorylation, Ubiquitination, and Methylation on the Binding of 53BP1 with Nucleosomes. Authors: Huasong Ai / Guo-Chao Chu / Qingyue Gong / Ze-Bin Tong / Zhiheng Deng / Xin Liu / Fan Yang / Ziyu Xu / Jia-Bin Li / Changlin Tian / Lei Liu / Abstract: The chemical synthesis of homogeneously modified histones is a powerful approach to quantitatively decipher how post-translational modifications (PTMs) modulate epigenetic events. Herein, we describe ...The chemical synthesis of homogeneously modified histones is a powerful approach to quantitatively decipher how post-translational modifications (PTMs) modulate epigenetic events. Herein, we describe the expedient syntheses of a selection of phosphorylated and ubiquitinated H2AX proteins in a strategy integrating expressed protein hydrazinolysis and auxiliary-mediated protein ligation. These modified H2AX proteins were then used to discover that although H2AXS139 phosphorylation can enhance the binding of the DNA damage repair factor 53BP1 to either an unmodified nucleosome or that bearing a single H2AXK15ub or H4K20me2 modification, it augments 53BP1's binding only weakly to nucleosomes bearing both H2AXK15ub and H4K20me2. To better understand why such a trivalent additive effect is lacking, we solved the cryo-EM structure (3.38 Å) of the complex of 53BP1 with the H2AXK15ub/S139ph_H4K20me2 nucleosome, which showed that H2AXS139 phosphorylation distorts the interaction interface between ubiquitin and 53BP1's UDR motif. Our study revealed that there is redundancy in the interplay of multiple histone PTMs, which may be useful for controlling the dynamic distribution of effector proteins onto nucleosomes bearing different histone variants and PTMs in a time-dependent fashion, through specific cellular biochemical events. | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34028.map.gz | 4.6 MB | EMDB map data format | |
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Header (meta data) | emd-34028-v30.xml emd-34028.xml | 25.8 KB 25.8 KB | Display Display | EMDB header |
Images | emd_34028.png | 132.1 KB | ||
Filedesc metadata | emd-34028.cif.gz | 6.6 KB | ||
Others | emd_34028_additional_1.map.gz emd_34028_half_map_1.map.gz emd_34028_half_map_2.map.gz | 49.5 MB 49.7 MB 49.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34028 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34028 | HTTPS FTP |
-Validation report
Summary document | emd_34028_validation.pdf.gz | 681.4 KB | Display | EMDB validaton report |
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Full document | emd_34028_full_validation.pdf.gz | 681 KB | Display | |
Data in XML | emd_34028_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | emd_34028_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34028 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34028 | HTTPS FTP |
-Related structure data
Related structure data | 7yqkMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_34028.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_34028_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34028_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34028_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Complex of 53BP1(1484-1972) and gammaH2AXK15ub-H4K20me2 nucleosome
+Supramolecule #1: Complex of 53BP1(1484-1972) and gammaH2AXK15ub-H4K20me2 nucleosome
+Macromolecule #1: Histone H3.1
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2AX
+Macromolecule #4: Histone H2B
+Macromolecule #7: Polyubiquitin-B
+Macromolecule #8: UDR motif of 53BP1
+Macromolecule #9: TP53-binding protein 1
+Macromolecule #5: DNA (145-MER)
+Macromolecule #6: DNA (145-MER)
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90830 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |