- EMDB-38101: Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub n... -
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Basic information
Entry
Database: EMDB / ID: EMD-38101
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)
Map data
Sample
Complex: cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination)
Protein or peptide: Histone H3.2
Protein or peptide: Histone H4
Protein or peptide: Histone H2A type 1-B/E
Protein or peptide: Histone H2B type 1-K
Protein or peptide: Histone H2A type 1-B/E
DNA: DNA (143-MER)
DNA: DNA (143-MER)
Protein or peptide: Ubiquitin-conjugating enzyme E2 D3
Protein or peptide: E3 ubiquitin-protein ligase RNF168
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
Entire : cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub n...
Entire
Name: cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination)
Components
Complex: cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination)
Protein or peptide: Histone H3.2
Protein or peptide: Histone H4
Protein or peptide: Histone H2A type 1-B/E
Protein or peptide: Histone H2B type 1-K
Protein or peptide: Histone H2A type 1-B/E
DNA: DNA (143-MER)
DNA: DNA (143-MER)
Protein or peptide: Ubiquitin-conjugating enzyme E2 D3
Protein or peptide: E3 ubiquitin-protein ligase RNF168
Ligand: ZINC ION
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Supramolecule #1: cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub n...
Supramolecule
Name: cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)
Organism: Homo sapiens (human)
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Macromolecule #1: Histone H3.2
Macromolecule
Name: Histone H3.2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
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