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Yorodumi- EMDB-16936: cGAS-Nucleosome in complex with SPSB3-ELOBC (composite structure) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16936 | |||||||||
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Title | cGAS-Nucleosome in complex with SPSB3-ELOBC (composite structure) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | cGAS / degradation / UPS / IMMUNE SYSTEM | |||||||||
Function / homology | Function and homology information cyclic GMP-AMP synthase / 2',3'-cyclic GMP-AMP synthase activity / STING mediated induction of host immune responses / target-directed miRNA degradation / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / elongin complex / VCB complex / cGAS/STING signaling pathway / regulation of immunoglobulin production ...cyclic GMP-AMP synthase / 2',3'-cyclic GMP-AMP synthase activity / STING mediated induction of host immune responses / target-directed miRNA degradation / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / elongin complex / VCB complex / cGAS/STING signaling pathway / regulation of immunoglobulin production / Cul5-RING ubiquitin ligase complex / regulation of T cell activation / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / pattern recognition receptor signaling pathway / STAT family protein binding / negative regulation of double-strand break repair via homologous recombination / negative regulation of cGAS/STING signaling pathway / cellular response to exogenous dsRNA / cytoplasmic pattern recognition receptor signaling pathway / ubiquitin-like protein ligase binding / cGMP-mediated signaling / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / cAMP-mediated signaling / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / nucleosome binding / positive regulation of type I interferon production / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Formation of HIV elongation complex in the absence of HIV Tat / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation 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 / positive regulation of defense response to virus by host / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / RNA Polymerase II Pre-transcription Events / Inhibition of DNA recombination at telomere / phosphatidylinositol-4,5-bisphosphate binding / Meiotic synapsis / telomere organization / activation of innate immune response / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / molecular condensate scaffold activity / DNA methylation / Condensation of Prophase Chromosomes / transcription corepressor binding / 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 / Defective pyroptosis / HDACs deacetylate histones / transcription elongation by RNA polymerase II / determination of adult lifespan / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Vif-mediated degradation of APOBEC3G / 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 / NoRC negatively regulates rRNA expression / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / HDMs demethylate histones / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Regulation of expression of SLITs and ROBOs / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / UCH proteinases / positive regulation of cellular senescence / nucleosome / protein-macromolecule adaptor activity Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Xu PB / Ablasser A | |||||||||
Funding support | European Union, 1 items
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Citation | Journal: Nature / Year: 2024 Title: The CRL5-SPSB3 ubiquitin ligase targets nuclear cGAS for degradation. Authors: Pengbiao Xu / Ying Liu / Chong Liu / Baptiste Guey / Lingyun Li / Pauline Melenec / Jonathan Ricci / Andrea Ablasser / Abstract: Cyclic GMP-AMP synthase (cGAS) senses aberrant DNA during infection, cancer and inflammatory disease, and initiates potent innate immune responses through the synthesis of 2'3'-cyclic GMP-AMP (cGAMP). ...Cyclic GMP-AMP synthase (cGAS) senses aberrant DNA during infection, cancer and inflammatory disease, and initiates potent innate immune responses through the synthesis of 2'3'-cyclic GMP-AMP (cGAMP). The indiscriminate activity of cGAS towards DNA demands tight regulatory mechanisms that are necessary to maintain cell and tissue homeostasis under normal conditions. Inside the cell nucleus, anchoring to nucleosomes and competition with chromatin architectural proteins jointly prohibit cGAS activation by genomic DNA. However, the fate of nuclear cGAS and its role in cell physiology remains unclear. Here we show that the ubiquitin proteasomal system (UPS) degrades nuclear cGAS in cycling cells. We identify SPSB3 as the cGAS-targeting substrate receptor that associates with the cullin-RING ubiquitin ligase 5 (CRL5) complex to ligate ubiquitin onto nuclear cGAS. A cryo-electron microscopy structure of nucleosome-bound cGAS in a complex with SPSB3 reveals a highly conserved Asn-Asn (NN) minimal degron motif at the C terminus of cGAS that directs SPSB3 recruitment, ubiquitylation and cGAS protein stability. Interference with SPSB3-regulated nuclear cGAS degradation primes cells for type I interferon signalling, conferring heightened protection against infection by DNA viruses. Our research defines protein degradation as a determinant of cGAS regulation in the nucleus and provides structural insights into an element of cGAS that is amenable to therapeutic exploitation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16936.map.gz | 43 MB | EMDB map data format | |
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Header (meta data) | emd-16936-v30.xml emd-16936.xml | 22.2 KB 22.2 KB | Display Display | EMDB header |
Images | emd_16936.png | 61.3 KB | ||
Filedesc metadata | emd-16936.cif.gz | 7.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16936 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16936 | HTTPS FTP |
-Related structure data
Related structure data | 8ol1MC 8okxC C: citing same article (ref.) M: atomic model generated by this map |
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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_16936.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.268 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : cGAS-Spsb3-EloBC complex
+Supramolecule #1: cGAS-Spsb3-EloBC complex
+Macromolecule #1: Histone H3.2
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A type 1-H
+Macromolecule #4: Histone H2B type 1-H
+Macromolecule #5: Histone H2A type 1-J
+Macromolecule #6: Histone H2B type 1-N
+Macromolecule #9: Cyclic GMP-AMP synthase
+Macromolecule #10: SPRY domain-containing SOCS box protein 3
+Macromolecule #11: Elongin-C
+Macromolecule #12: Elongin-B
+Macromolecule #7: DNA (145-MER)
+Macromolecule #8: DNA (145-MER)
+Macromolecule #13: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 / Details: PBS buffer |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL In silico model: alphafold2 prediction of individual proteins |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 592494 |