PDB-7a08: CryoEM Structure of cGAS Nucleosome complex

Basic information

• Entry: Database: PDB / ID: 7a08
• Title: CryoEM Structure of cGAS Nucleosome complex

Components

• (Nucleosomal DNA strand ...) x 2
• Cyclic GMP-AMP synthase
• Histone H2A type 1-C
• Histone H2B type 1-C/E/F/G/I
• Histone H3.3
• Histone H4

• Keywords: TRANSFERASE / complex / immune protein / nuclear protein

Function / homology

Function:

negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / regulation of type I interferon production / cyclic GMP-AMP synthase / 2',3'-cyclic GMP-AMP synthase activity / muscle cell differentiation / pericentric heterochromatin formation / inner kinetochore / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / negative regulation of DNA repair / regulation of immunoglobulin production / cGAS/STING signaling pathway / oocyte maturation / regulation of T cell activation / negative regulation of cGAS/STING signaling pathway / cGMP-mediated signaling / nucleus organization / cellular response to exogenous dsRNA / spermatid development / single fertilization / regulation of immune response / subtelomeric heterochromatin formation / positive regulation of type I interferon production / negative regulation of megakaryocyte differentiation / RNA polymerase II core promoter sequence-specific DNA binding / protein localization to CENP-A containing chromatin / negative regulation of double-strand break repair via homologous recombination / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / heterochromatin organization / Packaging Of Telomere Ends / nucleosome binding / 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 / 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 / Inhibition of DNA recombination at telomere / Meiotic synapsis / phosphatidylinositol-4,5-bisphosphate binding / telomere organization / activation of innate immune response / embryo implantation / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / cAMP-mediated signaling / 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 / molecular condensate scaffold activity / PRC2 methylates histones and DNA / innate immune response in mucosa / Defective pyroptosis / HDACs deacetylate histones / determination of adult lifespan / RNA Polymerase I Promoter Escape / 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 / 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 / multicellular organism growth / 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 / osteoblast differentiation / structural constituent of chromatin / antimicrobial humoral immune response mediated by antimicrobial peptide / UCH proteinases / positive regulation of cellular senescence / male gonad development / nucleosome / nucleosome assembly / 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 / site of double-strand break / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Processing of DNA double-strand break ends / antibacterial humoral response

Domain/homology:

Mab-21-like, nucleotidyltransferase domain / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21 protein nucleotidyltransferase domain / Mab-21-like / Mab-21 / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold

Component:

DNA / DNA (> 10) / DNA (> 100) / Histone H4 / Histone H2B type 1-C/E/F/G/I / Histone H3.3 / Cyclic GMP-AMP synthase / Histone H2A type 1-C

• Biological species: Mus musculus (house mouse); Homo sapiens (human); synthetic construct (others)
• Method: ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.11 Å
• Authors: Michalski, S. / de Oliveira Mann, C.C. / Witte, G. / Bartho, J. / Lammens, K. / Hopfner, K.P.

Funding support

Germany, 1items

Organization	Grant number	Country
German Research Foundation (DFG)	CRC/TRR237	Germany

• Citation: Journal: Nature / Year: 2020; Title: Structural basis for sequestration and autoinhibition of cGAS by chromatin.; Authors: Sebastian Michalski / Carina C de Oliveira Mann / Che A Stafford / Gregor Witte / Joseph Bartho / Katja Lammens / Veit Hornung / Karl-Peter Hopfner / ; Abstract: Cyclic GMP-AMP synthase (cGAS) is an innate immune sensor for cytosolic microbial DNA. After binding DNA, cGAS synthesizes the messenger 2'3'-cyclic GMP-AMP (cGAMP), which triggers cell-autonomous defence and the production of type I interferons and pro-inflammatory cytokines via the activation of STING. In addition to responding to cytosolic microbial DNA, cGAS also recognizes mislocalized cytosolic self-DNA and has been implicated in autoimmunity and sterile inflammation. Specificity towards pathogen- or damage-associated DNA was thought to be caused by cytosolic confinement. However, recent findings place cGAS robustly in the nucleus, where tight tethering of chromatin is important to prevent autoreactivity to self-DNA. Here we show how cGAS is sequestered and inhibited by chromatin. We provide a cryo-electron microscopy structure of the cGAS catalytic domain bound to a nucleosome, which shows that cGAS does not interact with the nucleosomal DNA, but instead interacts with histone 2A-histone 2B, and is tightly anchored to the 'acidic patch'. The interaction buries the cGAS DNA-binding site B, and blocks the formation of active cGAS dimers. The acidic patch robustly outcompetes agonistic DNA for binding to cGAS, which suggests that nucleosome sequestration can efficiently inhibit cGAS, even when accessible DNA is nearby, such as in actively transcribed genomic regions. Our results show how nuclear cGAS is sequestered by chromatin and provides a mechanism for preventing autoreactivity to nuclear self-DNA.

History

Deposition	Aug 7, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 23, 2020	Provider: repository / Type: Initial release
Revision 1.1	Dec 9, 2020	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Feb 10, 2021	Group: Source and taxonomy / Category: em_entity_assembly_naturalsource / Item: _em_entity_assembly_naturalsource.organism