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Yorodumi- EMDB-41801: Cryo-EM structure of the human nucleosome core particle ubiquityl... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41801 | |||||||||
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Title | Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 2) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Nucleosome core particle / chromatin / RNF168 / UbcH5c / DNA repair / DNA double-strand break / Homologous recombination / BRCA1-BARD1 / 53BP1 / ubiquitin / STRUCTURAL PROTEIN-DNA-TRANSFERASE complex | |||||||||
Function / homology | Function and homology information histone H2AK15 ubiquitin ligase activity / histone ubiquitin ligase activity / (E3-independent) E2 ubiquitin-conjugating enzyme / protein K6-linked ubiquitination / Signaling by BMP / isotype switching / double-strand break repair via classical nonhomologous end joining / protein K11-linked ubiquitination / DNA repair-dependent chromatin remodeling / K63-linked polyubiquitin modification-dependent protein binding ...histone H2AK15 ubiquitin ligase activity / histone ubiquitin ligase activity / (E3-independent) E2 ubiquitin-conjugating enzyme / protein K6-linked ubiquitination / Signaling by BMP / isotype switching / double-strand break repair via classical nonhomologous end joining / protein K11-linked ubiquitination / DNA repair-dependent chromatin remodeling / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / response to ionizing radiation / negative regulation of transcription elongation by RNA polymerase II / ubiquitin conjugating enzyme activity / protein monoubiquitination / protein K63-linked ubiquitination / negative regulation of BMP signaling pathway / nucleosome binding / negative regulation of tumor necrosis factor-mediated signaling pathway / protein K48-linked ubiquitination / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / protein autoubiquitination / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / interstrand cross-link repair / ubiquitin ligase complex / epigenetic regulation of gene expression / SUMOylation of DNA damage response and repair proteins / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / positive regulation of DNA repair / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / TICAM1, RIP1-mediated IKK complex recruitment / DNA methylation / Condensation of Prophase Chromosomes / IKK complex recruitment mediated by RIP1 / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / PRC2 methylates histones and DNA / innate immune response in mucosa / ubiquitin binding / Defective pyroptosis / HDACs deacetylate histones / Negative regulators of DDX58/IFIH1 signaling / RNA Polymerase I Promoter Escape / Peroxisomal protein import / Nonhomologous End-Joining (NHEJ) / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / lipopolysaccharide binding / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / protein modification process / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RING-type E3 ubiquitin transferase / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / Inactivation of CSF3 (G-CSF) signaling / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / double-strand break repair via nonhomologous end joining / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / protein polyubiquitination / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / ubiquitin-protein transferase activity / UCH proteinases / ubiquitin protein ligase activity / double-strand break repair / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Hu Q / Botuyan MV / Zhao D / Cui G / Mer G | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Mol Cell / Year: 2024 Title: Mechanisms of RNF168 nucleosome recognition and ubiquitylation. Authors: Qi Hu / Debiao Zhao / Gaofeng Cui / Janarjan Bhandari / James R Thompson / Maria Victoria Botuyan / Georges Mer / Abstract: RNF168 plays a central role in the DNA damage response (DDR) by ubiquitylating histone H2A at K13 and K15. These modifications direct BRCA1-BARD1 and 53BP1 foci formation in chromatin, essential for ...RNF168 plays a central role in the DNA damage response (DDR) by ubiquitylating histone H2A at K13 and K15. These modifications direct BRCA1-BARD1 and 53BP1 foci formation in chromatin, essential for cell-cycle-dependent DNA double-strand break (DSB) repair pathway selection. The mechanism by which RNF168 catalyzes the targeted accumulation of H2A ubiquitin conjugates to form repair foci around DSBs remains unclear. Here, using cryoelectron microscopy (cryo-EM), nuclear magnetic resonance (NMR) spectroscopy, and functional assays, we provide a molecular description of the reaction cycle and dynamics of RNF168 as it modifies the nucleosome and recognizes its ubiquitylation products. We demonstrate an interaction of a canonical ubiquitin-binding domain within full-length RNF168, which not only engages ubiquitin but also the nucleosome surface, clarifying how such site-specific ubiquitin recognition propels a signal amplification loop. Beyond offering mechanistic insights into a key DDR protein, our study aids in understanding site specificity in both generating and interpreting chromatin ubiquitylation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41801.map.gz | 4.8 MB | EMDB map data format | |
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Header (meta data) | emd-41801-v30.xml emd-41801.xml | 29 KB 29 KB | Display Display | EMDB header |
Images | emd_41801.png | 157.4 KB | ||
Masks | emd_41801_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-41801.cif.gz | 7.5 KB | ||
Others | emd_41801_additional_1.map.gz emd_41801_half_map_1.map.gz emd_41801_half_map_2.map.gz | 40.1 MB 49.8 MB 49.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41801 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41801 | HTTPS FTP |
-Related structure data
Related structure data | 8u14MC 8smwC 8smxC 8smyC 8smzC 8sn0C 8sn1C 8sn2C 8sn3C 8sn4C 8sn5C 8sn6C 8sn7C 8sn8C 8sn9C 8snaC 8txvC 8txwC 8txxC 8u13C 8upfC 8uq8C 8uq9C 8uqaC 8uqbC 8uqcC 8uqdC 8uqeC C: citing same article (ref.) M: atomic model generated by this map |
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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_41801.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: 1.0276 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_41801_msk_1.map | ||||||||||||
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Density Histograms |
-Additional map: #1
File | emd_41801_additional_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_41801_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_41801_half_map_2.map | ||||||||||||
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Density Histograms |
-Sample components
+Entire : Human nucleosome core particle ubiquitylated at histone H2A lysin...
+Supramolecule #1: Human nucleosome core particle ubiquitylated at histone H2A lysin...
+Macromolecule #1: Histone H3.1
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2B type 1-J
+Macromolecule #6: E3 ubiquitin-protein ligase RNF168
+Macromolecule #7: Ubiquitin-conjugating enzyme E2 D3
+Macromolecule #8: Histone H2A type 1-B/E
+Macromolecule #4: DNA (147-MER)
+Macromolecule #5: DNA (146-MER)
+Macromolecule #9: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
Details | 10 mM HEPES, 100 mM NaCl, 1 mM DTT, pH 7.5 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 5697 / Average electron dose: 50.0 e/Å2 Details: 5697 images were recorded in movie mode. 5503 were retained for particle picking. |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 9989935 |
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Startup model | Type of model: NONE |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1) |
Final 3D classification | Number classes: 3 / Software - Name: RELION (ver. 3.0.7) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1) |
Final reconstruction | Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.7) / Number images used: 27986 |
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT | ||||||||||||
Output model | PDB-8u14: |