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Yorodumi- PDB-8hsb: Cryo-EM Structure of CdnG-E2 complex from Serratia marcescens (Ul... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hsb | ||||||
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Title | Cryo-EM Structure of CdnG-E2 complex from Serratia marcescens (UltrAuFoil) | ||||||
Components |
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Keywords | ANTIVIRAL PROTEIN / cGAS / CdnG / E2 / CBASS | ||||||
Function / homology | Uncharacterized protein Function and homology information | ||||||
Biological species | Serratia marcescens (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Xiao, J. / Wang, L. | ||||||
Funding support | 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hsb.cif.gz | 104.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hsb.ent.gz | 79.8 KB | Display | PDB format |
PDBx/mmJSON format | 8hsb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hsb_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8hsb_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8hsb_validation.xml.gz | 30.4 KB | Display | |
Data in CIF | 8hsb_validation.cif.gz | 41.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hs/8hsb ftp://data.pdbj.org/pub/pdb/validation_reports/hs/8hsb | HTTPS FTP |
-Related structure data
Related structure data | 34992MC 8yjyC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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) |
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#2: 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 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: CdnG-E2 binary complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Serratia marcescens (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1100 nm |
Image recording | Electron dose: 70 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19_4092: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 512003 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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