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- PDB-7c0m: Human cGAS-nucleosome complex -

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Basic information

Entry
Database: PDB / ID: 7c0m
TitleHuman cGAS-nucleosome complex
Components
  • (DNA (145-MER)) x 2
  • Cyclic GMP-AMP synthase
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3.1Histone H3
  • Histone H4
KeywordsDNA BINDING PROTEIN/DNA / complex / chromatin / NTase / innate immunity / immunity / nucleosome / cGAS / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


cyclic GMP-AMP synthase / positive regulation of cGMP-mediated signaling / cyclic-GMP-AMP synthase activity / regulation of immunoglobulin production / paracrine signaling / negative regulation of double-strand break repair via homologous recombination / regulation of T cell activation / positive regulation of cAMP-mediated signaling / cellular response to exogenous dsRNA / negative regulation of megakaryocyte differentiation ...cyclic GMP-AMP synthase / positive regulation of cGMP-mediated signaling / cyclic-GMP-AMP synthase activity / regulation of immunoglobulin production / paracrine signaling / negative regulation of double-strand break repair via homologous recombination / regulation of T cell activation / positive regulation of cAMP-mediated signaling / cellular response to exogenous dsRNA / negative regulation of megakaryocyte differentiation / positive regulation of defense response to virus by host / CENP-A containing nucleosome assembly / activation of innate immune response / negative regulation of tumor necrosis factor-mediated signaling pathway / DNA replication-independent nucleosome assembly / telomere capping / interleukin-7-mediated signaling pathway / chromatin silencing / determination of adult lifespan / positive regulation of type I interferon production / telomere organization / DNA replication-dependent nucleosome assembly / innate immune response in mucosa / nuclear nucleosome / rDNA heterochromatin assembly / negative regulation of gene expression, epigenetic / regulation of gene silencing by miRNA / regulation of gene silencing / nuclear chromosome / DNA-templated transcription, initiation / regulation of megakaryocyte differentiation / phosphatidylinositol-4,5-bisphosphate binding / nucleosome assembly / lipopolysaccharide binding / nucleosome / site of double-strand break / positive regulation of cellular senescence / double-strand break repair via nonhomologous end joining / defense response to virus / double-stranded DNA binding / chromatin organization / nuclear chromosome, telomeric region / killing of cells of other organism / antibacterial humoral response / antimicrobial humoral immune response mediated by antimicrobial peptide / blood coagulation / protein ubiquitination / cadherin binding / defense response to Gram-negative bacterium / protein heterodimerization activity / defense response to Gram-positive bacterium / negative regulation of cell population proliferation / nuclear chromatin / DNA repair / protein domain specific binding / GTP binding / cellular response to DNA damage stimulus / chromatin binding / cellular protein metabolic process / innate immune response / viral process / host cell nucleus / protein-containing complex / RNA binding / DNA binding / extracellular space / extracellular exosome / membrane / extracellular region / nucleoplasm / ATP binding / plasma membrane / metal ion binding / nucleus / cytosol
Histone H3/CENP-A / TATA box binding protein associated factor (TAF) / CENP-T/Histone H4, histone fold / Histone H2A conserved site / Histone H2A, C-terminal domain / Mab-21 domain / Histone H4, conserved site / Histone-fold / Histone H2B / Histone H2A/H2B/H3 ...Histone H3/CENP-A / TATA box binding protein associated factor (TAF) / CENP-T/Histone H4, histone fold / Histone H2A conserved site / Histone H2A, C-terminal domain / Mab-21 domain / Histone H4, conserved site / Histone-fold / Histone H2B / Histone H2A/H2B/H3 / Histone H4 / Histone H2A
Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H4 / Histone H3.1 / Cyclic GMP-AMP synthase
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsKujirai, T. / Zierhut, C. / Takizawa, Y. / Kim, R. / Negishi, L. / Uruma, N. / Hirai, S. / Funabiki, H. / Kurumizaka, H.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP17H01408 Japan
Japan Society for the Promotion of Science (JSPS)JP18H05534 Japan
Japan Society for the Promotion of Science (JSPS)JP19K06522 Japan
Japan Science and TechnologyJPMJCR16G1 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101076 Japan
Japan Science and TechnologyJPMJER1901 Japan
CitationJournal: Science / Year: 2020
Title: Structural basis for the inhibition of cGAS by nucleosomes.
Authors: Tomoya Kujirai / Christian Zierhut / Yoshimasa Takizawa / Ryan Kim / Lumi Negishi / Nobuki Uruma / Seiya Hirai / Hironori Funabiki / Hitoshi Kurumizaka /
Abstract: The cyclic GMP-AMP synthase (cGAS) senses invasion of pathogenic DNA and stimulates inflammatory signaling, autophagy and apoptosis. Organization of host DNA into nucleosomes was proposed to limit ...The cyclic GMP-AMP synthase (cGAS) senses invasion of pathogenic DNA and stimulates inflammatory signaling, autophagy and apoptosis. Organization of host DNA into nucleosomes was proposed to limit cGAS autoinduction, but the underlying mechanism was unknown. Here, we report the structural basis for this inhibition. In the cryo-EM structure of the human cGAS-nucleosome core particle (NCP) complex, two cGAS monomers bridge two NCPs by binding the acidic patch of H2A-H2B and nucleosomal DNA. In this configuration, all three known cGAS DNA-binding sites, required for cGAS activation, are repurposed or become inaccessible, and cGAS dimerization, another prerequisite for activation, is inhibited. Mutating key residues linking cGAS and the acidic patch alleviates nucleosomal inhibition. This study establishes a structural framework for why cGAS is silenced on chromatinized self-DNA.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMay 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Histone H3.1
B: Histone H4
C: Histone H2A type 1-B/E
D: Histone H2B type 1-J
E: Histone H3.1
F: Histone H4
G: Histone H2A type 1-B/E
H: Histone H2B type 1-J
I: DNA (145-MER)
J: DNA (145-MER)
K: Cyclic GMP-AMP synthase
a: Histone H3.1
b: Histone H4
c: Histone H2A type 1-B/E
d: Histone H2B type 1-J
e: Histone H3.1
f: Histone H4
g: Histone H2A type 1-B/E
h: Histone H2B type 1-J
i: DNA (145-MER)
j: DNA (145-MER)
k: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)492,27124
Polymers492,14022
Non-polymers1312
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area117000 Å2
ΔGint-805 kcal/mol
Surface area173670 Å2

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Components

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Protein , 5 types, 18 molecules AEaeBFbfCGcgDHdhKk

#1: Protein
Histone H3.1 / Histone H3 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 15719.445 Da / Num. of mol.: 4
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
#2: Protein
Histone H4 /


Mass: 11676.703 Da / Num. of mol.: 4
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, H4-16, HIST4H4
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#3: Protein
Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 14447.825 Da / Num. of mol.: 4
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
#4: Protein
Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 14217.516 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2BC11, H2BFR, HIST1H2BJ / Production host: Escherichia coli (E. coli) / References: UniProt: P06899
#7: Protein Cyclic GMP-AMP synthase / / h-cGAS / 2'3'-cGAMP synthase / Mab-21 domain-containing protein 1


Mass: 44435.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CGAS, C6orf150, MB21D1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N884, cyclic GMP-AMP synthase

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DNA chain , 2 types, 4 molecules IiJj

#5: DNA chain DNA (145-MER)


Mass: 44520.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#6: DNA chain DNA (145-MER)


Mass: 44991.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 1 types, 2 molecules

#8: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human cGAS-nucleosome complex / Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 64 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 160075 / Symmetry type: POINT

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