+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34274 | |||||||||
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Title | Bre1-nucleosome complex | |||||||||
Map data | 3DFlex map | |||||||||
Sample |
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Keywords | transcription / ubiquitin ligase / cancer / chromatin / GENE REGULATION / GENE REGULATION-DNA complex | |||||||||
Function / homology | Function and homology information histone H2B C-terminal K residue ubiquitin ligase activity / HULC complex / RHOBTB1 GTPase cycle / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / heterochromatin organization ...histone H2B C-terminal K residue ubiquitin ligase activity / HULC complex / RHOBTB1 GTPase cycle / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / heterochromatin organization / epigenetic regulation of gene expression / Packaging Of Telomere Ends / ubiquitin ligase complex / 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 / 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 / negative regulation of cell migration / DNA methylation / 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 / PRC2 methylates histones and DNA / innate immune response in mucosa / Defective pyroptosis / mRNA 3'-UTR binding / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Nonhomologous End-Joining (NHEJ) / 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 / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / 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 / 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 / nucleosome assembly / p53 binding / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / Processing of DNA double-strand break ends / histone binding / antibacterial humoral response / Senescence-Associated Secretory Phenotype (SASP) / ubiquitin-dependent protein catabolic process / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / Estrogen-dependent gene expression / killing of cells of another organism / chromosome, telomeric region / transcription coactivator activity / Ub-specific processing proteases / defense response to Gram-positive bacterium / protein ubiquitination / cadherin binding / neuron projection / protein heterodimerization activity / Amyloid fiber formation / ubiquitin protein ligase binding / chromatin binding / regulation of DNA-templated transcription / nucleolus / positive regulation of DNA-templated transcription / enzyme binding / protein homodimerization activity Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.81 Å | |||||||||
Authors | Onishi S / Hamada K / Sato K / Nishizawa T / Nureki O / Ogata K / Sengoku T | |||||||||
Funding support | Japan, 1 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structure of the human Bre1 complex bound to the nucleosome. Authors: Shuhei Onishi / Kotone Uchiyama / Ko Sato / Chikako Okada / Shunsuke Kobayashi / Keisuke Hamada / Tomohiro Nishizawa / Osamu Nureki / Kazuhiro Ogata / Toru Sengoku / Abstract: Histone H2B monoubiquitination (at Lys120 in humans) regulates transcription elongation and DNA repair. In humans, H2B monoubiquitination is catalyzed by the heterodimeric Bre1 complex composed of ...Histone H2B monoubiquitination (at Lys120 in humans) regulates transcription elongation and DNA repair. In humans, H2B monoubiquitination is catalyzed by the heterodimeric Bre1 complex composed of Bre1A/RNF20 and Bre1B/RNF40. The Bre1 proteins generally function as tumor suppressors, while in certain cancers, they facilitate cancer cell proliferation. To obtain structural insights of H2BK120 ubiquitination and its regulation, we report the cryo-electron microscopy structure of the human Bre1 complex bound to the nucleosome. The two RING domains of Bre1A and Bre1B recognize the acidic patch and the nucleosomal DNA phosphates around SHL 6.0-6.5, which are ideally located to recruit the E2 enzyme and ubiquitin for H2BK120-specific ubiquitination. Mutational experiments suggest that the two RING domains bind in two orientations and that ubiquitination occurs when Bre1A binds to the acidic patch. Our results provide insights into the H2BK120-specific ubiquitination by the Bre1 proteins and suggest that H2B monoubiquitination can be regulated by nuclesomal DNA flexibility. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34274.map.gz | 116.9 MB | EMDB map data format | |
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Header (meta data) | emd-34274-v30.xml emd-34274.xml | 27.8 KB 27.8 KB | Display Display | EMDB header |
Images | emd_34274.png | 181.7 KB | ||
Filedesc metadata | emd-34274.cif.gz | 7.7 KB | ||
Others | emd_34274_additional_1.map.gz emd_34274_half_map_1.map.gz emd_34274_half_map_2.map.gz | 63 MB 2.1 MB 2.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34274 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34274 | HTTPS FTP |
-Validation report
Summary document | emd_34274_validation.pdf.gz | 480.6 KB | Display | EMDB validaton report |
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Full document | emd_34274_full_validation.pdf.gz | 480.2 KB | Display | |
Data in XML | emd_34274_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | emd_34274_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34274 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34274 | HTTPS FTP |
-Related structure data
Related structure data | 8guiMC 8gujMC 8gukC 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_34274.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | 3DFlex map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: NU-refinement map
File | emd_34274_additional_1.map | ||||||||||||
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Annotation | NU-refinement map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: 3DFlex half map
File | emd_34274_half_map_1.map | ||||||||||||
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Annotation | 3DFlex half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: 3DFlex half map
File | emd_34274_half_map_2.map | ||||||||||||
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Annotation | 3DFlex half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Bre1-nucleosome complex
+Supramolecule #1: Bre1-nucleosome complex
+Supramolecule #2: Histone
+Supramolecule #3: DNA
+Supramolecule #4: Bre1
+Macromolecule #1: Histone H3.1
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A type 1
+Macromolecule #4: Histone H2B type 1-J
+Macromolecule #7: E3 ubiquitin-protein ligase BRE1A
+Macromolecule #8: E3 ubiquitin-protein ligase BRE1B
+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
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 BIOQUANTUM (6k x 4k) / Average electron dose: 58.0 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: 1.8 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 83000 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |