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Yorodumi- EMDB-40606: Cryo-EM structure of the human nucleosome core particle in comple... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40606 | |||||||||
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Title | Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 3) | |||||||||
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Sample |
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Keywords | Nucleosome core particle / chromatin / RNF168 / RING domain / UbcH5c / DNA repair / DNA double-strand break / Homologous recombination / 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 / Signaling by BMP / protein K6-linked ubiquitination / double-strand break repair via classical nonhomologous end joining / isotype switching / protein K11-linked ubiquitination / DNA repair-dependent chromatin remodeling / positive regulation of protein targeting to mitochondrion ...histone H2AK15 ubiquitin ligase activity / histone ubiquitin ligase activity / (E3-independent) E2 ubiquitin-conjugating enzyme / Signaling by BMP / protein K6-linked ubiquitination / double-strand break repair via classical nonhomologous end joining / isotype switching / protein K11-linked ubiquitination / DNA repair-dependent chromatin remodeling / positive regulation of protein targeting to mitochondrion / K63-linked polyubiquitin modification-dependent protein binding / E2 ubiquitin-conjugating enzyme / response to ionizing radiation / negative regulation of transcription elongation by RNA polymerase II / protein monoubiquitination / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / negative regulation of BMP signaling pathway / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / protein autoubiquitination / protein K48-linked ubiquitination / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / interstrand cross-link repair / SUMOylation of DNA damage response and repair proteins / heterochromatin organization / epigenetic regulation of gene expression / Packaging Of Telomere Ends / ubiquitin ligase complex / nucleosome binding / 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 / nucleosomal DNA binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / positive regulation of DNA repair / 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 / IKK complex recruitment mediated by RIP1 / 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 / innate immune response in mucosa / PRC2 methylates histones and DNA / ubiquitin binding / Defective pyroptosis / Negative regulators of DDX58/IFIH1 signaling / HDACs deacetylate histones / Peroxisomal protein import / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Nonhomologous End-Joining (NHEJ) / Regulation of TNFR1 signaling / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RING-type E3 ubiquitin transferase / protein modification process / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / 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 / double-strand break repair via nonhomologous end joining / Transcriptional regulation of granulopoiesis / protein polyubiquitination / structural constituent of chromatin / antimicrobial humoral immune response mediated by antimicrobial peptide / ubiquitin-protein transferase activity / UCH proteinases / ubiquitin protein ligase activity / nucleosome / double-strand break repair / nucleosome assembly / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 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_40606.map.gz | 59.5 MB | EMDB map data format | |
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Header (meta data) | emd-40606-v30.xml emd-40606.xml | 29.7 KB 29.7 KB | Display Display | EMDB header |
Images | emd_40606.png | 151.9 KB | ||
Masks | emd_40606_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-40606.cif.gz | 7.6 KB | ||
Others | emd_40606_additional_1.map.gz emd_40606_half_map_1.map.gz emd_40606_half_map_2.map.gz | 32.5 MB 59.3 MB 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40606 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40606 | HTTPS FTP |
-Validation report
Summary document | emd_40606_validation.pdf.gz | 872.3 KB | Display | EMDB validaton report |
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Full document | emd_40606_full_validation.pdf.gz | 871.9 KB | Display | |
Data in XML | emd_40606_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | emd_40606_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40606 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40606 | HTTPS FTP |
-Related structure data
Related structure data | 8smyMC 8smwC 8smxC 8smzC 8sn0C 8sn1C 8sn2C 8sn3C 8sn4C 8sn5C 8sn6C 8sn7C 8sn8C 8sn9C 8snaC 8txvC 8txwC 8txxC 8u13C 8u14C 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_40606.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: 1.328 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_40606_msk_1.map | ||||||||||||
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Density Histograms |
-Additional map: #1
File | emd_40606_additional_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_40606_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_40606_half_map_2.map | ||||||||||||
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Density Histograms |
-Sample components
+Entire : Human nucleosome core particle in complex with RNF168 and UbcH5c~Ub
+Supramolecule #1: Human nucleosome core particle in complex with RNF168 and UbcH5c~Ub
+Macromolecule #1: Histone H3.1
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A type 1-B/E
+Macromolecule #4: Histone H2B type 1-J
+Macromolecule #7: E3 ubiquitin-protein ligase RNF168
+Macromolecule #8: Ubiquitin-conjugating enzyme E2 D3
+Macromolecule #5: DNA (147-MER)
+Macromolecule #6: DNA (147-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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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 14179 / Average electron dose: 60.0 e/Å2 Details: 14179 images were recorded in movie-mode of which 14113 were retained for particle picking. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT | ||||||||
Output model | PDB-8smy: |