+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-39353 | |||||||||
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Title | Cryo-EM Structure of CdnG-E2 complex from Serratia marcescens | |||||||||
Map data | ||||||||||
Sample |
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Keywords | cGAS / CdnG / E2 / CBASS / ANTIVIRAL PROTEIN | |||||||||
Function / homology | Uncharacterized protein Function and homology information | |||||||||
Biological species | Serratia marcescens (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Xiao J / Wang L | |||||||||
Funding support | 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_39353.map.gz | 167.7 MB | EMDB map data format | |
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Header (meta data) | emd-39353-v30.xml emd-39353.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
Images | emd_39353.png | 90.6 KB | ||
Filedesc metadata | emd-39353.cif.gz | 5.6 KB | ||
Others | emd_39353_half_map_1.map.gz emd_39353_half_map_2.map.gz | 165.4 MB 165.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-39353 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-39353 | HTTPS FTP |
-Related structure data
Related structure data | 8yjyMC 8hsbC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_39353.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.67 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_39353_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_39353_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : CdnG-E2 binary complex
Entire | Name: CdnG-E2 binary complex |
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Components |
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-Supramolecule #1: CdnG-E2 binary complex
Supramolecule | Name: CdnG-E2 binary complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Serratia marcescens (bacteria) |
-Macromolecule #1: SmCdnG
Macromolecule | Name: SmCdnG / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Serratia marcescens (bacteria) |
Molecular weight | Theoretical: 45.481707 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #2: Type VI secretion protein
Macromolecule | Name: Type VI secretion protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Serratia marcescens (bacteria) |
Molecular weight | Theoretical: 18.78267 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MNNVVIRHHC KPLTIAQQYR ALKAGGPYER LRIIHHDRTL LWEGWLQPSL FSRRYKVAVR YSLGTPPICV VTEPDLFALA GTRAIPHLY PADKHIPGAR LCLFLPRSQA DDGLSEWRAQ LKISDTLIPW ASLWLFYFEQ WLHTGHWEGG GKHPRPSEVK N ER UniProtKB: Uncharacterized protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 263744 |