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- EMDB-70483: Cryo-EM structure of cGAS tetramer in complex with BuDNA (bubble DNA) -

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Basic information

Entry
Database: EMDB / ID: EMD-70483
TitleCryo-EM structure of cGAS tetramer in complex with BuDNA (bubble DNA)
Map data
Sample
  • Complex: The structure of mouse cGAS in complex with a bubble DNA
    • Complex: mouse cGAS
      • Protein or peptide: Cyclic GMP-AMP synthase
    • Complex: The forward strand of bubble DNA
      • DNA: Bubble DNA Forward(41-MER)
    • Complex: The reverse strand of bubble DNA
      • DNA: Bubble DNA Reverse(41-MER)
  • Ligand: ZINC ION
KeywordsComplex / Activator / TRANSFERASE-DNA complex
Function / homology
Function and homology information


: / 2',3'-cyclic GMP-AMP synthase activity / cyclic GMP-AMP synthase / regulation of type I interferon production / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / regulation of immunoglobulin production / : / regulation of T cell activation / cGAS/STING signaling pathway ...: / 2',3'-cyclic GMP-AMP synthase activity / cyclic GMP-AMP synthase / regulation of type I interferon production / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / regulation of immunoglobulin production / : / regulation of T cell activation / cGAS/STING signaling pathway / pattern recognition receptor signaling pathway / negative regulation of DNA repair / negative regulation of cGAS/STING signaling pathway / cellular response to exogenous dsRNA / cytoplasmic pattern recognition receptor signaling pathway / regulation of immune response / negative regulation of double-strand break repair via homologous recombination / nucleosome binding / positive regulation of defense response to virus by host / positive regulation of type I interferon production / phosphatidylinositol-4,5-bisphosphate binding / activation of innate immune response / determination of adult lifespan / molecular condensate scaffold activity / positive regulation of cellular senescence / site of double-strand break / double-stranded DNA binding / defense response to virus / nuclear body / innate immune response / DNA repair / DNA damage response / chromatin binding / GTP binding / protein homodimerization activity / DNA binding / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Mab-21-like, nucleotidyltransferase domain / Mab-21 protein nucleotidyltransferase domain / Mab-21-like / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21
Similarity search - Domain/homology
Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesMus musculus (house mouse) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.48 Å
AuthorsWu S / Sohn J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM129342 United States
CitationJournal: To Be Published
Title: The Cryo-EM structure of cGAS tetramer in complex with BuDNA (bubble DNA)
Authors: Wu S / Sohn J
History
DepositionMay 2, 2025-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70483.png

Downloads & links

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Map

FileDownload / File: emd_70483.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 400 pix.
= 372. Å		0.93 Å/pix.
x 400 pix.
= 372. Å		0.93 Å/pix.
x 400 pix.
= 372. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.115
Minimum - Maximum-0.89519435 - 1.2657944
Average (Standard dev.)-0.00008288414 (±0.020916358)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 372.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70483_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_70483_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_70483_half_map_2.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 : The structure of mouse cGAS in complex with a bubble DNA

EntireName: The structure of mouse cGAS in complex with a bubble DNA
Components
  • Complex: The structure of mouse cGAS in complex with a bubble DNA
    • Complex: mouse cGAS
      • Protein or peptide: Cyclic GMP-AMP synthase
    • Complex: The forward strand of bubble DNA
      • DNA: Bubble DNA Forward(41-MER)
    • Complex: The reverse strand of bubble DNA
      • DNA: Bubble DNA Reverse(41-MER)
  • Ligand: ZINC ION

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Supramolecule #1: The structure of mouse cGAS in complex with a bubble DNA

SupramoleculeName: The structure of mouse cGAS in complex with a bubble DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Complex generated by incubating mouse cGAS with a bubble DNA.
Molecular weightTheoretical: 222 KDa

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Supramolecule #2: mouse cGAS

SupramoleculeName: mouse cGAS / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: The forward strand of bubble DNA

SupramoleculeName: The forward strand of bubble DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 / Details: Bubble DNA Forward oligo DNA sequence
Source (natural)Organism: synthetic construct (others)

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Supramolecule #4: The reverse strand of bubble DNA

SupramoleculeName: The reverse strand of bubble DNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3 / Details: Bubble DNA Reverse oligo DNA sequence
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Cyclic GMP-AMP synthase

MacromoleculeName: Cyclic GMP-AMP synthase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: cyclic GMP-AMP synthase
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 41.970508 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: KLKKVLDKLR LKRKDISEAA ETVNKVVERL LRRMQKRESE FKGVEQLNTG SYYEHVKISA PNEFDVMFKL EVPRIELQEY YETGAFYLV KFKRIPRGNP LSHFLEGEVL SATKMLSKFR KIIKEEVKEI KDIDVSVEKE KPGSPAVTLL IRNPEEISVD I ILALESKG ...String:
KLKKVLDKLR LKRKDISEAA ETVNKVVERL LRRMQKRESE FKGVEQLNTG SYYEHVKISA PNEFDVMFKL EVPRIELQEY YETGAFYLV KFKRIPRGNP LSHFLEGEVL SATKMLSKFR KIIKEEVKEI KDIDVSVEKE KPGSPAVTLL IRNPEEISVD I ILALESKG SWPISTKEGL PIQGWLGTKV RTNLRREPFY LVPKNAKDGN SFQGETWRLS FSHTEKYILN NHGIEKTCCE SS GAKCCRK ECLKLMKYLL EQLKKEFQEL DAFCSYHVKT AIFHMWTQDP QDSQWDPRNL SSCFDKLLAF FLECLRTEKL DHY FIPKFN LFSQELIDRK SKEFLSKKIE YERNNGFPIF D

UniProtKB: Cyclic GMP-AMP synthase

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Macromolecule #2: Bubble DNA Forward(41-MER)

MacromoleculeName: Bubble DNA Forward(41-MER) / type: dna / ID: 2 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 12.694225 KDa
SequenceString:
(DC)(DA)(DC)(DA)(DG)(DA)(DG)(DA)(DA)(DG) (DA)(DA)(DC)(DA)(DT)(DT)(DT)(DG)(DA)(DC) (DC)(DC)(DG)(DG)(DG)(DT)(DA)(DA)(DA) (DG)(DC)(DT)(DA)(DA)(DT)(DA)(DA)(DC)(DA) (DA) (DG)

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Macromolecule #3: Bubble DNA Reverse(41-MER)

MacromoleculeName: Bubble DNA Reverse(41-MER) / type: dna / ID: 3 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 12.546035 KDa
SequenceString:
(DC)(DT)(DT)(DG)(DT)(DT)(DA)(DT)(DT)(DA) (DG)(DC)(DT)(DT)(DT)(DA)(DC)(DC)(DC)(DG) (DG)(DG)(DT)(DC)(DA)(DA)(DA)(DT)(DG) (DT)(DT)(DC)(DT)(DT)(DC)(DT)(DC)(DT)(DG) (DT) (DG)

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

Concentration1.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMtris(hydroxymethyl)aminomethane
150.0 mMsodium chlorideNaCl
0.5 mMtris(2-carboxyethyl)phosphine

Details: 20mM Tris pH 7.5, 150mM NaCl, and 0.5mM TCEP
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 120 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.00037 kPa
Details: Glow-discharged with a PELCO easiGlow Cryo-EM Glow Discharge Set (TED PELLA, INC.) with settings as follow: Plasma Current 15 mA, Process Timer 60s, Working Vacuum 0.37mBar, Preprocess Hold ...Details: Glow-discharged with a PELCO easiGlow Cryo-EM Glow Discharge Set (TED PELLA, INC.) with settings as follow: Plasma Current 15 mA, Process Timer 60s, Working Vacuum 0.37mBar, Preprocess Hold Timer 10s, and negative polarity.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: Filter paper blotted with blot force 2 and blot time 2s, and plunge-frozen in liquid ethane using a Vitrobot Mark IV at 4 degree Celsius and 100% humidity..
DetailsThe complex was prepared using a gel filtration column(HiLoadTM 16/600 SuperdexTM 200pg,Cytiva).

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 9927 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2969717
Details: A total of 2,969,717 particles were auto-picked using Blob Picker in CryoSPARC.
CTF correctionSoftware - Name: cryoSPARC (ver. v4.3.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5n6i

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.3.1) / Details: Particles are randomly split into two halves. / Number images used: 62441
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.3.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. v4.3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

5n6i

chain_id: A, source_name: PDB, initial_model_type: experimental model

5n6i

chain_id: B, source_name: PDB, initial_model_type: experimental model

5n6i

chain_id: C, source_name: PDB, initial_model_type: experimental model

5n6i

chain_id: D, source_name: PDB, initial_model_type: experimental model

5n6i

chain_id: G, source_name: PDB, initial_model_type: experimental model

5n6i

chain_id: H, source_name: PDB, initial_model_type: experimental model

5n6i

chain_id: I, source_name: PDB, initial_model_type: experimental model

5n6i

chain_id: J, source_name: PDB, initial_model_type: experimental model
DetailsInitial local fitting was done using UCSF ChimeraX, and then COOT was used for manual building.
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 87.5 / Target criteria: Cross-correlation coefficient
Output model

PDB-9oh4:
Cryo-EM structure of cGAS tetramer in complex with BuDNA (bubble DNA)

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