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- EMDB-39353: Cryo-EM Structure of CdnG-E2 complex from Serratia marcescens -

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Basic information

Entry
Database: EMDB / ID: EMD-39353
TitleCryo-EM Structure of CdnG-E2 complex from Serratia marcescens
Map data
Sample
  • Complex: CdnG-E2 binary complex
    • Protein or peptide: SmCdnG
    • Protein or peptide: Type VI secretion protein
KeywordscGAS / CdnG / E2 / CBASS / ANTIVIRAL PROTEIN
Function / homologyUncharacterized protein
Function and homology information
Biological speciesSerratia marcescens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsXiao J / Wang L
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Microbiol / Year: 2024
Title: Phage defence system CBASS is regulated by a prokaryotic E2 enzyme that imitates the ubiquitin pathway.
Authors: Yan Yan / Jun Xiao / Fengtao Huang / Wei Xian / Bingbing Yu / Rui Cheng / Hui Wu / Xueling Lu / Xionglue Wang / Wenjing Huang / Jing Li / Greater Kayode Oyejobi / Carol V Robinson / Hao Wu / ...Authors: Yan Yan / Jun Xiao / Fengtao Huang / Wei Xian / Bingbing Yu / Rui Cheng / Hui Wu / Xueling Lu / Xionglue Wang / Wenjing Huang / Jing Li / Greater Kayode Oyejobi / Carol V Robinson / Hao Wu / Di Wu / Xiaoyun Liu / Longfei Wang / Bin Zhu /
Abstract: The cyclic-oligonucleotide-based anti-phage signalling system (CBASS) is a type of innate prokaryotic immune system. Composed of a cyclic GMP-AMP synthase (cGAS) and CBASS-associated proteins, CBASS ...The cyclic-oligonucleotide-based anti-phage signalling system (CBASS) is a type of innate prokaryotic immune system. Composed of a cyclic GMP-AMP synthase (cGAS) and CBASS-associated proteins, CBASS uses cyclic oligonucleotides to activate antiviral immunity. One major class of CBASS contains a homologue of eukaryotic ubiquitin-conjugating enzymes, which is either an E1-E2 fusion or a single E2. However, the functions of single E2s in CBASS remain elusive. Here, using biochemical, genetic, cryo-electron microscopy and mass spectrometry investigations, we discover that the E2 enzyme from Serratia marcescens regulates cGAS by imitating the ubiquitination cascade. This includes the processing of the cGAS C terminus, conjugation of cGAS to a cysteine residue, ligation of cGAS to a lysine residue, cleavage of the isopeptide bond and poly-cGASylation. The poly-cGASylation activates cGAS to produce cGAMP, which acts as an antiviral signal and leads to cell death. Thus, our findings reveal a unique regulatory role of E2 in CBASS.
History
DepositionMar 3, 2024-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39353.png

Downloads & links

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Map

FileDownload / File: emd_39353.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 360 pix.
= 241.2 Å		0.67 Å/pix.
x 360 pix.
= 241.2 Å		0.67 Å/pix.
x 360 pix.
= 241.2 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.67 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.67799944 - 0.91229093
Average (Standard dev.)-0.00006226579 (±0.013644989)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 241.20001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39353_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_39353_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : CdnG-E2 binary complex

EntireName: CdnG-E2 binary complex
Components
  • Complex: CdnG-E2 binary complex
    • Protein or peptide: SmCdnG
    • Protein or peptide: Type VI secretion protein

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Supramolecule #1: CdnG-E2 binary complex

SupramoleculeName: CdnG-E2 binary complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Serratia marcescens (bacteria)

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Macromolecule #1: SmCdnG

MacromoleculeName: SmCdnG / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Serratia marcescens (bacteria)
Molecular weightTheoretical: 45.481707 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MYGSTTARNL PSGKKQRIAD LLSQIIETLD LTKTQYANIE SAYNGVGTFL SEGDDPLLQD AVIYPQGSVR LNTTVKPKNE EQYDIDLIC YLPHATQADY TGVISAIRQR LESHKTYKTL LSELPRGFRI NYAGDYHLDI TPGRDHTGTA HPGQPLWVVD A QTAWKESN ...String:
MYGSTTARNL PSGKKQRIAD LLSQIIETLD LTKTQYANIE SAYNGVGTFL SEGDDPLLQD AVIYPQGSVR LNTTVKPKNE EQYDIDLIC YLPHATQADY TGVISAIRQR LESHKTYKTL LSELPRGFRI NYAGDYHLDI TPGRDHTGTA HPGQPLWVVD A QTAWKESN PSGYAEWFES SASVQPLRTI LVMDSASRVG TEALLPLPDS TDKKLLNHIV QILKRHRDEW AAEQDEVRQR CR PISVIIT TLACHAYNHI IADRRAYDND LDILLDVLEL MPDFIVSTQG AIHVNNPHMP EENFAEKWNR SEQDEGPQRS EAF YQWHAA AQATFNTIAA SVGEDNLFLS LEDSFGKTPV DVVRQRLMEH MQSAREQGSL HLDKKTGGLI ATGLAGTAAQ AGVP KNTFY GE

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Macromolecule #2: Type VI secretion protein

MacromoleculeName: Type VI secretion protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Serratia marcescens (bacteria)
Molecular weightTheoretical: 18.78267 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MNNVVIRHHC KPLTIAQQYR ALKAGGPYER LRIIHHDRTL LWEGWLQPSL FSRRYKVAVR YSLGTPPICV VTEPDLFALA GTRAIPHLY PADKHIPGAR LCLFLPRSQA DDGLSEWRAQ LKISDTLIPW ASLWLFYFEQ WLHTGHWEGG GKHPRPSEVK N ER

UniProtKB: Uncharacterized protein

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 263744
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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