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Yorodumi- EMDB-38101: Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub n... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38101 | |||||||||
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Title | Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination) | |||||||||
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Keywords | RNF168 / nucleosome / H2AK13/15 ubiquitination / NUCLEAR PROTEIN / NUCLEAR PROTEIN-DNA 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 / isotype switching / double-strand break repair via classical nonhomologous end joining / protein K11-linked ubiquitination / DNA repair-dependent chromatin remodeling / negative regulation of BMP signaling pathway ...histone H2AK15 ubiquitin ligase activity / histone ubiquitin ligase activity / (E3-independent) E2 ubiquitin-conjugating enzyme / Signaling by BMP / protein K6-linked ubiquitination / isotype switching / double-strand break repair via classical nonhomologous end joining / protein K11-linked ubiquitination / DNA repair-dependent chromatin remodeling / negative regulation of BMP signaling pathway / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / K63-linked polyubiquitin modification-dependent protein binding / response to ionizing radiation / negative regulation of transcription elongation by RNA polymerase II / protein monoubiquitination / protein localization to CENP-A containing chromatin / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / CENP-A containing nucleosome / Replacement of protamines by nucleosomes in the male pronucleus / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / positive regulation of DNA repair / nucleosome binding / Packaging Of Telomere Ends / protein K48-linked ubiquitination / protein autoubiquitination / lipoxygenase pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / arachidonate metabolic process / Chromatin modifying enzymes / lipid oxidation / SUMOylation of DNA damage response and repair proteins / interstrand cross-link repair / Deposition of new CENPA-containing nucleosomes at the centromere / hepoxilin biosynthetic process / ubiquitin ligase complex / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / linoleic acid metabolic process / Meiotic synapsis / Inhibition of DNA recombination at telomere / nucleosomal DNA binding / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Interleukin-7 signaling / epigenetic regulation of gene expression / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / TICAM1, RIP1-mediated IKK complex recruitment / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / IKK complex recruitment mediated by RIP1 / Defective pyroptosis / Meiotic recombination / innate immune response in mucosa / DNA Damage/Telomere Stress Induced Senescence / ubiquitin binding / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Negative regulators of DDX58/IFIH1 signaling / Transcriptional regulation by small RNAs / Transcriptional regulation of granulopoiesis / Peroxisomal protein import / HDMs demethylate histones / Regulation of TNFR1 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PKMTs methylate histone lysines / protein modification process / RING-type E3 ubiquitin transferase / B-WICH complex positively regulates rRNA expression / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / heterochromatin formation / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / Activation of anterior HOX genes in hindbrain development during early embryogenesis / double-strand break repair via nonhomologous end joining / structural constituent of chromatin / protein polyubiquitination / ubiquitin-protein transferase activity / UCH proteinases / nucleosome / ubiquitin protein ligase activity / antimicrobial humoral immune response mediated by antimicrobial peptide / double-strand break repair / Factors involved in megakaryocyte development and platelet production Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.27 Å | |||||||||
Authors | Ai HS / Tong ZB / Deng ZH / Pan M / Liu L | |||||||||
Funding support | China, 1 items
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Citation | Journal: Biorxiv / Year: 2024 Title: Capturing Snapshots of Nucleosomal H2A K13/K15 Ubiquitination Mediated by the Monomeric E3 Ligase RNF168 Authors: Ai H / Tong Z / Deng Z / Shi Q / Tao S / Liang J / Sun M / Wu X / Zheng Q / Liang L / Li JB / Gao S / Tian C / Liu L / Pan M | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38101.map.gz | 3.8 MB | EMDB map data format | |
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Header (meta data) | emd-38101-v30.xml emd-38101.xml | 25.6 KB 25.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_38101_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_38101.png | 64.3 KB | ||
Masks | emd_38101_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-38101.cif.gz | 6.8 KB | ||
Others | emd_38101_additional_1.map.gz emd_38101_half_map_1.map.gz emd_38101_half_map_2.map.gz | 2.5 MB 49.7 MB 49.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38101 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38101 | HTTPS FTP |
-Validation report
Summary document | emd_38101_validation.pdf.gz | 711.3 KB | Display | EMDB validaton report |
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Full document | emd_38101_full_validation.pdf.gz | 710.8 KB | Display | |
Data in XML | emd_38101_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | emd_38101_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38101 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38101 | HTTPS FTP |
-Related structure data
Related structure data | 8x7kMC 8x7iC 8x7jC 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_38101.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: 1.074 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_38101_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Cryo-EM map of RNF168/UbcH5c-Ub/monoubiquitinated nucleosome complex at a...
File | emd_38101_additional_1.map | ||||||||||||
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Annotation | Cryo-EM map of RNF168/UbcH5c-Ub/monoubiquitinated nucleosome complex at a resolution of 6.2 angstrom | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_38101_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_38101_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub n...
+Supramolecule #1: cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub n...
+Macromolecule #1: Histone H3.2
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A type 1-B/E
+Macromolecule #4: Histone H2B type 1-K
+Macromolecule #5: Histone H2A type 1-B/E
+Macromolecule #8: Ubiquitin-conjugating enzyme E2 D3
+Macromolecule #9: E3 ubiquitin-protein ligase RNF168
+Macromolecule #6: DNA (143-MER)
+Macromolecule #7: DNA (143-MER)
+Macromolecule #10: ZINC ION
-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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |