+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30340 | ||||||||||||||||||||||||
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Title | Structure of the 2:2 cGAS-nucleosome complex | ||||||||||||||||||||||||
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Keywords | cGAS / nucleosome / inhibition / cryo-EM / IMMUNE SYSTEM / STRUCTURAL PROTEIN-TRANSFERASE-DNA complex | ||||||||||||||||||||||||
Function / homology | Function and homology information cyclic GMP-AMP synthase / 2',3'-cyclic GMP-AMP synthase activity / STING mediated induction of host immune responses / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / regulation of immunoglobulin production / cGAS/STING signaling pathway / pattern recognition receptor signaling pathway / regulation of T cell activation / cytoplasmic pattern recognition receptor signaling pathway ...cyclic GMP-AMP synthase / 2',3'-cyclic GMP-AMP synthase activity / STING mediated induction of host immune responses / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / regulation of immunoglobulin production / cGAS/STING signaling pathway / pattern recognition receptor signaling pathway / regulation of T cell activation / cytoplasmic pattern recognition receptor signaling pathway / negative regulation of cGAS/STING signaling pathway / cGMP-mediated signaling / cellular response to exogenous dsRNA / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of type I interferon production / Replacement of protamines by nucleosomes in the male pronucleus / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / nucleosome binding / Packaging Of Telomere Ends / negative regulation of double-strand break repair via homologous recombination / 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 / 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 / positive regulation of defense response to virus by host / nucleosomal DNA binding / RNA Polymerase I Promoter Opening / phosphatidylinositol-4,5-bisphosphate binding / Assembly of the ORC complex at the origin of replication / activation of innate immune response / Interleukin-7 signaling / epigenetic regulation of gene expression / DNA methylation / cAMP-mediated signaling / 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 / molecular condensate scaffold activity / Defective pyroptosis / Meiotic recombination / innate immune response in mucosa / DNA Damage/Telomere Stress Induced Senescence / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / determination of adult lifespan / Transcriptional regulation by small RNAs / lipopolysaccharide binding / 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 / B-WICH complex positively regulates rRNA expression / heterochromatin formation / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / Activation of anterior HOX genes in hindbrain development during early embryogenesis / structural constituent of chromatin / positive regulation of cellular senescence / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / 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 / double-stranded DNA binding / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / site of double-strand break / gene expression / antibacterial humoral response / Oxidative Stress Induced Senescence / defense response to virus / defense response to Gram-negative bacterium Similarity search - Function | ||||||||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.9 Å | ||||||||||||||||||||||||
Authors | Cao D / Han X | ||||||||||||||||||||||||
Funding support | China, 7 items
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Citation | Journal: Cell Res / Year: 2020 Title: Structural basis for nucleosome-mediated inhibition of cGAS activity. Authors: Duanfang Cao / Xiaonan Han / Xiaoyi Fan / Rui-Ming Xu / Xinzheng Zhang / Abstract: Activation of cyclic GMP-AMP synthase (cGAS) through sensing cytosolic double stranded DNA (dsDNA) plays a pivotal role in innate immunity against exogenous infection as well as cellular regulation ...Activation of cyclic GMP-AMP synthase (cGAS) through sensing cytosolic double stranded DNA (dsDNA) plays a pivotal role in innate immunity against exogenous infection as well as cellular regulation under stress. Aberrant activation of cGAS induced by self-DNA is related to autoimmune diseases. cGAS accumulates at chromosomes during mitosis or spontaneously in the nucleus. Binding of cGAS to the nucleosome competitively attenuates the dsDNA-mediated cGAS activation, but the molecular mechanism of the attenuation is still poorly understood. Here, we report two cryo-electron microscopy structures of cGAS-nucleosome complexes. The structures reveal that cGAS interacts with the nucleosome as a monomer, forming 1:1 and 2:2 complexes, respectively. cGAS contacts the nucleosomal acidic patch formed by the H2A-H2B heterodimer through the dsDNA-binding site B in both complexes, and could interact with the DNA from the other symmetrically placed nucleosome via the dsDNA-binding site C in the 2:2 complex. The bound nucleosome inhibits the activation of cGAS through blocking the interaction of cGAS with ligand dsDNA and disrupting cGAS dimerization. R236A or R255A mutation of cGAS impairs the binding between cGAS and the nucleosome, and largely relieves the nucleosome-mediated inhibition of cGAS activity. Our study provides structural insights into the inhibition of cGAS activity by the nucleosome, and advances the understanding of the mechanism by which hosts avoid the autoimmune attack caused by cGAS. | ||||||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30340.map.gz | 85.2 MB | EMDB map data format | |
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Header (meta data) | emd-30340-v30.xml emd-30340.xml | 19.3 KB 19.3 KB | Display Display | EMDB header |
Images | emd_30340.png | 67.6 KB | ||
Filedesc metadata | emd-30340.cif.gz | 6.1 KB | ||
Others | emd_30340_additional_1.map.gz | 85.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30340 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30340 | HTTPS FTP |
-Related structure data
Related structure data | 7ccrMC 7ccqC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30340.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: #1
File | emd_30340_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : the cGAS-nucleosome complex in 2:2 molar ratio
Entire | Name: the cGAS-nucleosome complex in 2:2 molar ratio |
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Components |
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-Supramolecule #1: the cGAS-nucleosome complex in 2:2 molar ratio
Supramolecule | Name: the cGAS-nucleosome complex in 2:2 molar ratio / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Histone H3.1
Macromolecule | Name: Histone H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.504476 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: PHRYRPGTVA LREIRRYQKS TELLIRKLPF QRLVREIAQD FKTDLRFQSS AVMALQEACE AYLVGLFEDT NLCAIHAKRV TIMPKDIQL ARRIRGERA UniProtKB: Histone H3.1 |
-Macromolecule #2: Histone H4
Macromolecule | Name: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 9.067586 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: RDNIQGITKP AIRRLARRGG VKRISGLIYE ETRGVLKVFL ENVIRDAVTY TEHAKRKTVT AMDVVYALKR QGRTLYGFGG |
-Macromolecule #3: Histone H2A type 1-B/E
Macromolecule | Name: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.308161 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: KTRSSRAGLQ FPVGRVHRLL RKGNYSERVG AGAPVYLAAV LEYLTAEILE LAGNAARDNK KTRIIPRHLQ LAIRNDEELN KLLGRVTIA QGGVLPNIQA VLLP UniProtKB: Histone H2A type 1-B/E |
-Macromolecule #4: Histone H2B type 1-J
Macromolecule | Name: Histone H2B type 1-J / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 10.334827 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SRKESYSIYV YKVLKQVHPD TGISSKAMGI MNSFVNDIFE RIAGEASRLA HYNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTK YTSA UniProtKB: Histone H2B type 1-J |
-Macromolecule #7: Cyclic GMP-AMP synthase
Macromolecule | Name: Cyclic GMP-AMP synthase / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO / EC number: cyclic GMP-AMP synthase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 42.75927 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: DAAPGASKLR AVLEKLKLSR DDISTAAGMV KGVVDHLLLR LKCDSAFRGV GLLNTGSYYE HVKISAPNEF DVMFKLEVPR IQLEEYSNT RAYYFVKFKR NPKENPLSQF LEGEILSASK MLSKFRKIIK EEINDIKDTD VIMKRKRGGS PAVTLLISEK I SVDITLAL ...String: DAAPGASKLR AVLEKLKLSR DDISTAAGMV KGVVDHLLLR LKCDSAFRGV GLLNTGSYYE HVKISAPNEF DVMFKLEVPR IQLEEYSNT RAYYFVKFKR NPKENPLSQF LEGEILSASK MLSKFRKIIK EEINDIKDTD VIMKRKRGGS PAVTLLISEK I SVDITLAL ESKSSWPAST QEGLRIQNWL SAKVRKQLRL KPFYLVPKHA KEGNGFQEET WRLSFSHIEK EILNNHGKSK TC CENKEEK CCRKDCLKLM KYLLEQLKER FKDKKHLDKF SSYHVKTAFF HVCTQNPQDS QWDRKDLGLC FDNCVTYFLQ CLR TEKLEN YFIPEFNLFS SNLIDKRSKE FLTKQIEYER NNEFPVFDEF UniProtKB: Cyclic GMP-AMP synthase |
-Macromolecule #5: DNA (147-MER)
Macromolecule | Name: DNA (147-MER) / type: dna / ID: 5 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 45.604047 KDa |
Sequence | String: (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC) ...String: (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC) (DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT) (DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG) (DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC) (DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC)(DG) (DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT) (DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT) (DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC) (DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC)(DG) (DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC) (DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC)(DT) (DC)(DC)(DA)(DG) |
-Macromolecule #6: DNA (147-MER)
Macromolecule | Name: DNA (147-MER) / type: dna / ID: 6 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 45.145754 KDa |
Sequence | String: (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT) ...String: (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT) (DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT) (DA)(DA) (DA)(DC)(DG)(DC)(DA)(DC)(DG) (DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT) (DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT) (DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC) (DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT) (DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT) (DC)(DT)(DC)(DC)(DA) (DG)(DG)(DC)(DA) (DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC) (DC)(DT)(DG)(DT) |
-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 TECNAI ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 107374 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |