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- PDB-8hsb: Cryo-EM Structure of CdnG-E2 complex from Serratia marcescens (Ul... -

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Basic information

Entry
Database: PDB / ID: 8hsb
TitleCryo-EM Structure of CdnG-E2 complex from Serratia marcescens (UltrAuFoil)
Components
  • CdnG
  • Type VI secretion protein
KeywordsANTIVIRAL PROTEIN / cGAS / CdnG / E2 / CBASS
Function / homologyUncharacterized protein
Function and homology information
Biological speciesSerratia marcescens (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsXiao, J. / Wang, L.
Funding support1items
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
DepositionDec 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
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Revision 1.1Jun 19, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jun 25, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 25, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CdnG
B: Type VI secretion protein


Theoretical massNumber of molelcules
Total (without water)64,2642
Polymers64,2642
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein CdnG


Mass: 45481.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Production host: Escherichia coli (E. coli)
#2: Protein Type VI secretion protein


Mass: 18782.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: AR325_02475, AR325_06795 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P0QAP1
Has protein modificationN

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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: CdnG-E2 binary complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Serratia marcescens (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 70 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19_4092: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 512003 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034389
ELECTRON MICROSCOPYf_angle_d0.6375970
ELECTRON MICROSCOPYf_dihedral_angle_d5.187584
ELECTRON MICROSCOPYf_chiral_restr0.044649
ELECTRON MICROSCOPYf_plane_restr0.006775

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