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- EMDB-40607: Cryo-EM structure of the human nucleosome core particle in comple... -
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Basic information
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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 4) | |||||||||
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![]() | 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 | ![]() histone H2AK15 ubiquitin ligase activity / histone ubiquitin ligase activity / Signaling by BMP / protein K6-linked ubiquitination / (E3-independent) E2 ubiquitin-conjugating enzyme / double-strand break repair via classical nonhomologous end joining / isotype switching / protein K11-linked ubiquitination / positive regulation of protein targeting to mitochondrion / K63-linked polyubiquitin modification-dependent protein binding ...histone H2AK15 ubiquitin ligase activity / histone ubiquitin ligase activity / Signaling by BMP / protein K6-linked ubiquitination / (E3-independent) E2 ubiquitin-conjugating enzyme / double-strand break repair via classical nonhomologous end joining / isotype switching / protein K11-linked ubiquitination / positive regulation of protein targeting to mitochondrion / K63-linked polyubiquitin modification-dependent protein binding / E2 ubiquitin-conjugating enzyme / response to ionizing radiation / DNA repair-dependent chromatin remodeling / ubiquitin conjugating enzyme activity / negative regulation of transcription elongation by RNA polymerase II / protein K63-linked ubiquitination / negative regulation of BMP signaling pathway / protein monoubiquitination / negative regulation of tumor necrosis factor-mediated signaling pathway / ubiquitin ligase complex / interstrand cross-link repair / SUMOylation of DNA damage response and repair proteins / negative regulation of megakaryocyte differentiation / protein K48-linked ubiquitination / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / nucleosome binding / Replacement of protamines by nucleosomes in the male pronucleus / protein autoubiquitination / CENP-A containing nucleosome / Packaging Of Telomere Ends / TICAM1, RIP1-mediated IKK complex recruitment / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / 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 / telomere organization / Interleukin-7 signaling / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / Negative regulators of DDX58/IFIH1 signaling / positive regulation of DNA repair / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / DNA methylation / Peroxisomal protein import / Condensation of Prophase Chromosomes / epigenetic regulation of gene expression / Chromatin modifications during the maternal to zygotic transition (MZT) / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SIRT1 negatively regulates rRNA expression / HCMV Late Events / Regulation of TNFR1 signaling / ubiquitin binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / innate immune response in mucosa / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDMs demethylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Inactivation of CSF3 (G-CSF) signaling / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / lipopolysaccharide binding / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / Metalloprotease DUBs / NoRC negatively regulates rRNA expression / RING-type E3 ubiquitin transferase / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / protein modification process / double-strand break repair via nonhomologous end joining / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / UCH proteinases / HCMV Early Events / protein polyubiquitination / ubiquitin-protein transferase activity / antimicrobial humoral immune response mediated by antimicrobial peptide / Antigen processing: Ubiquitination & Proteasome degradation / structural constituent of chromatin / ubiquitin protein ligase activity / antibacterial humoral response / E3 ubiquitin ligases ubiquitinate target proteins Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
![]() | Hu Q / Botuyan MV / Zhao D / Cui G / Mer G | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 59.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 29.7 KB 29.7 KB | Display Display | ![]() |
Images | ![]() | 158.1 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Filedesc metadata | ![]() | 7.5 KB | ||
Others | ![]() ![]() ![]() | 59.3 MB 59.3 MB 59.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 881.3 KB | Display | ![]() |
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Full document | ![]() | 880.9 KB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Data in CIF | ![]() | 14.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8smzMC ![]() 8smwC ![]() 8smxC ![]() 8smyC ![]() 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 ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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
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-Additional map: #1
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-Half map: #1
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-Half map: #2
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Density Histograms |
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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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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
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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: ![]() |
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 |
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Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT | ||||||||
Output model | ![]() PDB-8smz: |