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- EMDB-30267: Human cGAS-nucleosome complex -

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Basic information

Entry
Database: EMDB / ID: EMD-30267
TitleHuman cGAS-nucleosome complex
Map data
SampleHuman cGAS-nucleosome complex:
Histone H3.1Histone H3 / Histone H4 / Histone H2A type 1-B/E / Histone H2B type 1-J / (nucleic-acidNucleic acid) x 2 / Cyclic GMP-AMP synthase / ligand
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)
Methodsingle 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, 6 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP17H01408 Japan
Japan Society for the Promotion of Science (JSPS)JP19K06522 Japan
Japan Society for the Promotion of Science (JSPS)JP18H05534 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101076 Japan
Japan Science and TechnologyJPMJCR16G1 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 ReportPDB-ID: 7c0m

SummaryFull reportAbout validation report
History
DepositionMay 1, 2020-
Header (metadata) releaseSep 16, 2020-
Map releaseSep 16, 2020-
UpdateSep 23, 2020-
Current statusSep 23, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0119
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0119
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7c0m
  • Surface level: 0.0119
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_30267.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 250 pix.
= 262.5 Å
1.05 Å/pix.
x 250 pix.
= 262.5 Å
1.05 Å/pix.
x 250 pix.
= 262.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 0.0119 / Movie #1: 0.0119
Minimum - Maximum-0.015324667 - 0.058220237
Average (Standard dev.)0.0008259152 (±0.0035567656)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 262.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z262.500262.500262.500
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.0150.0580.001

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Supplemental data

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Sample components

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Entire Human cGAS-nucleosome complex

EntireName: Human cGAS-nucleosome complex / Number of components: 9

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Component #1: protein, Human cGAS-nucleosome complex

ProteinName: Human cGAS-nucleosome complex / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Histone H3.1

ProteinName: Histone H3.1Histone H3 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 15.719445 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, Histone H4

ProteinName: Histone H4 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 11.676703 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, Histone H2A type 1-B/E

ProteinName: Histone H2A type 1-B/E / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 14.447825 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, Histone H2B type 1-J

ProteinName: Histone H2B type 1-J / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 14.217516 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: nucleic-acid, DNA (145-MER)

nucleic acidName: DNA (145-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DA)(DT)(DC)(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) ...Sequence:
(DA)(DT)(DC)(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)(DG)(DA)(DT)
MassTheoretical: 44.520383 kDa
SourceSpecies: synthetic construct (others)

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Component #7: nucleic-acid, DNA (145-MER)

nucleic acidName: DNA (145-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DA)(DT)(DC)(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) ...Sequence:
(DA)(DT)(DC)(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)(DG)(DA)(DT)
MassTheoretical: 44.99166 kDa
SourceSpecies: synthetic construct (others)

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Component #8: protein, Cyclic GMP-AMP synthase

ProteinName: Cyclic GMP-AMP synthase / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 44.435191 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #9: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 64 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 160075
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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