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- EMDB-22413: 1:1 cGAS(mask)-NCP map -

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Basic information

Entry
Database: EMDB / ID: EMD-22413
Title1:1 cGAS(mask)-NCP map
Map data1:! cGAS(mask)-nucleosome map
Sample
  • Complex: 1:1 cGAS-nucleosome complex
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsBoyer JA / Spangler CJ / Strauss JD / McGinty RK / Zhang Q
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM133498 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R21CA234979 United States
CitationJournal: Science / Year: 2020
Title: Structural basis of nucleosome-dependent cGAS inhibition.
Authors: Joshua A Boyer / Cathy J Spangler / Joshua D Strauss / Andrew P Cesmat / Pengda Liu / Robert K McGinty / Qi Zhang /
Abstract: Cyclic guanosine monophosphate (GMP)-adenosine monophosphate (AMP) synthase (cGAS) recognizes cytosolic foreign or damaged DNA to activate the innate immune response to infection, inflammatory ...Cyclic guanosine monophosphate (GMP)-adenosine monophosphate (AMP) synthase (cGAS) recognizes cytosolic foreign or damaged DNA to activate the innate immune response to infection, inflammatory diseases, and cancer. By contrast, cGAS reactivity against self-DNA in the nucleus is suppressed by chromatin tethering. We report a 3.3-angstrom-resolution cryo-electron microscopy structure of cGAS in complex with the nucleosome core particle. The structure reveals that cGAS uses two conserved arginines to anchor to the nucleosome acidic patch. The nucleosome-binding interface exclusively occupies the strong double-stranded DNA (dsDNA)-binding surface on cGAS and sterically prevents cGAS from oligomerizing into the functionally active 2:2 cGAS-dsDNA state. These findings provide a structural basis for how cGAS maintains an inhibited state in the nucleus and further exemplify the role of the nucleosome in regulating diverse nuclear protein functions.
History
DepositionAug 7, 2020-
Header (metadata) releaseSep 16, 2020-
Map releaseSep 16, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22413.png

Downloads & links

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Map

FileDownload / File: emd_22413.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation1:! cGAS(mask)-nucleosome map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 330 pix.
= 300.3 Å		0.91 Å/pix.
x 330 pix.
= 300.3 Å		0.91 Å/pix.
x 330 pix.
= 300.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.044269003 - 0.08581101
Average (Standard dev.)0.0001613208 (±0.0017686688)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions330330330
Spacing330330330
CellA=B=C: 300.30002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.910.910.91
M x/y/z330330330
origin x/y/z0.0000.0000.000
length x/y/z300.300300.300300.300
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS330330330
D min/max/mean-0.0440.0860.000

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Supplemental data

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Additional map: 1:1 cGAS-nucleosome composite map

Fileemd_22413_additional.map
Annotation1:1 cGAS-nucleosome composite map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 1:1 cGAS-nucleosome composite map

Fileemd_22413_additional_1.map
Annotation1:1 cGAS-nucleosome composite map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 1:1 cGAS-nucleosome complex

EntireName: 1:1 cGAS-nucleosome complex
Components
  • Complex: 1:1 cGAS-nucleosome complex

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Supramolecule #1: 1:1 cGAS-nucleosome complex

SupramoleculeName: 1:1 cGAS-nucleosome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 / Details: mouse cGAS bound to the nucleosome in a 1:1 ratio
Molecular weightTheoretical: 250 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMNaClsodium chloride
1.0 mMC9H15O6PTCEP
GridModel: Quantifoil / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Details: Instrument: Pelco easiGlow
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 2100 / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 433445
CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6esf


Details: low-pass filtered to 50A
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1-beta) / Number images used: 44311
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1-beta)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1-beta)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model(PDB ID:

6fq5

,

4k8v

)
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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