8HSB | pdb_00008hsb

Cryo-EM Structure of CdnG-E2 complex from Serratia marcescens (UltrAuFoil)

• PDB DOI: https://doi.org/10.2210/pdb8HSB/pdb
• EM Map EMD-34992: EMDB EMDataResource

• Classification: ANTIVIRAL PROTEIN
• Organism(s): Serratia marcescens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-12-18 Released: 2024-05-01 
• Deposition Author(s): Xiao, J., Wang, L.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Phage defence system CBASS is regulated by a prokaryotic E2 enzyme that imitates the ubiquitin pathway.

Yan, Y., Xiao, J., Huang, F., Xian, W., Yu, B., Cheng, R., Wu, H., Lu, X., Wang, X., Huang, W., Li, J., Oyejobi, G.K., Robinson, C.V., Wu, H., Wu, D., Liu, X., Wang, L., Zhu, B.

(2024) Nat Microbiol 9: 1566-1578

• PubMed: 38649411 
• DOI: https://doi.org/10.1038/s41564-024-01684-z
• Primary Citation Related Structures: 
  8HSB, 8YJY


• PubMed 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 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.

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Organizational Affiliation: 
• Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
Department of Cardiovascular Surgery, Taikang Center for Life and Medical Sciences Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.
Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China. [e-mail].
Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China. [e-mail].
Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.
NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China.
Department of Chemistry, University of Oxford, Oxford, UK.
Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
Department of Chemistry, University of Oxford, Oxford, UK. [e-mail].
Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK. [e-mail].
Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China. [e-mail].
NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China. [e-mail].
Department of Cardiovascular Surgery, Taikang Center for Life and Medical Sciences Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China. [e-mail].
Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China. [e-mail].
Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 64.26 kDa 
• Atom Count: 4,278 
• Modeled Residue Count: 533 
• Deposited Residue Count: 569 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CdnG	A	407	Serratia marcescens	Mutation(s): 0
UniProt
Find proteins for A0AAT8XUL1 (Serratia marcescens) Explore A0AAT8XUL1  Go to UniProtKB:  A0AAT8XUL1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Type VI secretion protein	B	162	Serratia marcescens	Mutation(s): 0  Gene Names: AR325_02475, AR325_06795
UniProt
Find proteins for A0AAT8XUL2 (Serratia marcescens) Explore A0AAT8XUL2  Go to UniProtKB:  A0AAT8XUL2

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-05-01 
Deposition Author(s): Xiao, J., Wang, L.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-05-01
  Type: Initial release
  
• Version 1.1: 2024-06-19
  Changes: Database references
• Version 1.2: 2025-06-25
  Changes: Data collection, Structure summary