+Open data
-Basic information
Entry | Database: PDB / ID: 8iej | ||||||
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Title | RNF20-RNF40/hRad6A-Ub/nucleosome complex | ||||||
Components |
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Keywords | NUCLEAR PROTEIN / RNF20 / RFN40 / RAD6 / nucleosome / H2BK120Ub | ||||||
Function / homology | Function and homology information histone H2B C-terminal K residue ubiquitin ligase activity / HULC complex / positive regulation of mitophagy / protein K11-linked ubiquitination / postreplication repair / RHOBTB1 GTPase cycle / E2 ubiquitin-conjugating enzyme / protein localization to CENP-A containing chromatin / ubiquitin conjugating enzyme activity / CENP-A containing nucleosome ...histone H2B C-terminal K residue ubiquitin ligase activity / HULC complex / positive regulation of mitophagy / protein K11-linked ubiquitination / postreplication repair / RHOBTB1 GTPase cycle / E2 ubiquitin-conjugating enzyme / protein localization to CENP-A containing chromatin / ubiquitin conjugating enzyme activity / CENP-A containing nucleosome / Replacement of protamines by nucleosomes in the male pronucleus / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / Packaging Of Telomere Ends / protein K48-linked ubiquitination / lipoxygenase pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / telomere organization / arachidonate metabolic process / Chromatin modifying enzymes / lipid oxidation / Deposition of new CENPA-containing nucleosomes at the centromere / hepoxilin biosynthetic process / response to UV / 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 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Condensation of Prophase Chromosomes / HCMV Late Events / 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 / negative regulation of cell migration / Defective pyroptosis / Meiotic recombination / innate immune response in mucosa / DNA Damage/Telomere Stress Induced Senescence / ubiquitin binding / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / mRNA 3'-UTR binding / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Transcriptional regulation of granulopoiesis / HDMs demethylate histones / 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 / RING-type E3 ubiquitin transferase / B-WICH complex positively regulates rRNA expression / heterochromatin formation / p53 binding / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / G2/M transition of mitotic cell cycle / Activation of anterior HOX genes in hindbrain development during early embryogenesis / 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 / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / Antigen processing: Ubiquitination & Proteasome degradation / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / E3 ubiquitin ligases ubiquitinate target proteins / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / gene expression / antibacterial humoral response / histone binding / ubiquitin-dependent protein catabolic process / Oxidative Stress Induced Senescence / proteasome-mediated ubiquitin-dependent protein catabolic process / defense response to Gram-negative bacterium / Estrogen-dependent gene expression / transcription coactivator activity / killing of cells of another organism Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.12 Å | ||||||
Authors | Ai, H. / Deng, Z. / Sun, M. / Du, Y. / Pan, M. / Liu, L. | ||||||
Funding support | China, 1items
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Citation | Journal: Mol Cell / Year: 2023 Title: Mechanistic insights into nucleosomal H2B monoubiquitylation mediated by yeast Bre1-Rad6 and its human homolog RNF20/RNF40-hRAD6A. Authors: Zhiheng Deng / Huasong Ai / Maoshen Sun / Zebin Tong / Yunxiang Du / Qian Qu / Liying Zhang / Ziyu Xu / Shixian Tao / Qiang Shi / Jia-Bin Li / Man Pan / Lei Liu / Abstract: Histone H2B monoubiquitylation plays essential roles in chromatin-based transcriptional processes. A RING-type E3 ligase (yeast Bre1 or human RNF20/RNF40) and an E2 ubiquitin-conjugating enzyme ...Histone H2B monoubiquitylation plays essential roles in chromatin-based transcriptional processes. A RING-type E3 ligase (yeast Bre1 or human RNF20/RNF40) and an E2 ubiquitin-conjugating enzyme (yeast Rad6 or human hRAD6A), together, precisely deposit ubiquitin on H2B K123 in yeast or K120 in humans. Here, we developed a chemical trapping strategy and successfully captured the transient structures of Bre1- or RNF20/RNF40-mediated ubiquitin transfer from Rad6 or hRAD6A to nucleosomal H2B. Our structures show that Bre1 and RNF40 directly bind nucleosomal DNA, exhibiting a conserved E3/E2/nucleosome interaction pattern from yeast to humans for H2B monoubiquitylation. We also find an uncanonical non-hydrophobic contact in the Bre1 RING-Rad6 interface, which positions Rad6 directly above the target H2B lysine residue. Our study provides mechanistic insights into the site-specific monoubiquitylation of H2B, reveals a critical role of nucleosomal DNA in mediating E3 ligase recognition, and provides a framework for understanding the cancer-driving mutations of RNF20/RNF40. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8iej.cif.gz | 341.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8iej.ent.gz | 257.4 KB | Display | PDB format |
PDBx/mmJSON format | 8iej.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8iej_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8iej_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8iej_validation.xml.gz | 42.7 KB | Display | |
Data in CIF | 8iej_validation.cif.gz | 67.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/8iej ftp://data.pdbj.org/pub/pdb/validation_reports/ie/8iej | HTTPS FTP |
-Related structure data
Related structure data | 35383MC 8iegC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 4 types, 7 molecules CGEKFLR
#1: Protein | Mass: 11936.948 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE / Production host: Escherichia coli (E. coli) / References: UniProt: P04908 #3: Protein | Mass: 11562.577 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, ...Gene: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J Production host: Escherichia coli (E. coli) / References: UniProt: P68431 #4: Protein | Mass: 9123.692 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, ...Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4C16, H4-16, HIST4H4 Production host: Escherichia coli (E. coli) / References: UniProt: P62805 #10: Protein | | Mass: 17114.129 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2A, RAD6A / Production host: Escherichia coli (E. coli) References: UniProt: P49459, E2 ubiquitin-conjugating enzyme |
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-Histone H2B type 1- ... , 2 types, 2 molecules DH
#2: Protein | Mass: 10451.957 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: H2BC12, H2BFT, HIRIP1, HIST1H2BK / Production host: Escherichia coli (E. coli) / References: UniProt: O60814 |
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#5: Protein | Mass: 10477.994 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: H2BC12, H2BFT, HIRIP1, HIST1H2BK / Production host: Escherichia coli (E. coli) / References: UniProt: O60814 |
-DNA chain , 2 types, 2 molecules IJ
#6: DNA chain | Mass: 45604.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
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#7: DNA chain | Mass: 45145.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
-E3 ubiquitin-protein ligase ... , 2 types, 2 molecules AM
#8: Protein | Mass: 7120.409 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RNF40, BRE1B, KIAA0661 Production host: Mammalian expression vector Flag-MCS-pcDNA3.1 (others) References: UniProt: O75150, RING-type E3 ubiquitin transferase |
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#9: Protein | Mass: 7144.470 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RNF20, BRE1A Production host: Mammalian expression vector Flag-MCS-pcDNA3.1 (others) References: UniProt: Q5VTR2, RING-type E3 ubiquitin transferase |
-Non-polymers , 1 types, 4 molecules
#11: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: RNF20-RNF40/hRAD6A-Ub in complex with nucleosome / Type: COMPLEX / Entity ID: #1-#10 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 239429 / Symmetry type: POINT | ||||||||||||||||||||||||
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