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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Novel Anti-phage System | |||||||||
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![]() | Anti-Phage / IMMUNE SYSTEM | |||||||||
Function / homology | ![]() endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.66 Å | |||||||||
![]() | Li J / Wang Z / Wang L | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structures and activation mechanism of the Gabija anti-phage system. Authors: Jing Li / Rui Cheng / Zhiming Wang / Wuliu Yuan / Jun Xiao / Xinyuan Zhao / Xinran Du / Shiyu Xia / Lianrong Wang / Bin Zhu / Longfei Wang / ![]() ![]() Abstract: Prokaryotes have evolved intricate innate immune systems against phage infection. Gabija is a highly widespread prokaryotic defence system that consists of two components, GajA and GajB. GajA ...Prokaryotes have evolved intricate innate immune systems against phage infection. Gabija is a highly widespread prokaryotic defence system that consists of two components, GajA and GajB. GajA functions as a DNA endonuclease that is inactive in the presence of ATP. Here, to explore how the Gabija system is activated for anti-phage defence, we report its cryo-electron microscopy structures in five states, including apo GajA, GajA in complex with DNA, GajA bound by ATP, apo GajA-GajB, and GajA-GajB in complex with ATP and Mg. GajA is a rhombus-shaped tetramer with its ATPase domain clustered at the centre and the topoisomerase-primase (Toprim) domain located peripherally. ATP binding at the ATPase domain stabilizes the insertion region within the ATPase domain, keeping the Toprim domain in a closed state. Upon ATP depletion by phages, the Toprim domain opens to bind and cleave the DNA substrate. GajB, which docks on GajA, is activated by the cleaved DNA, ultimately leading to prokaryotic cell death. Our study presents a mechanistic landscape of Gabija activation. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 197.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.1 KB 14.1 KB | Display Display | ![]() |
Images | ![]() | 79.7 KB | ||
Filedesc metadata | ![]() | 5.3 KB | ||
Others | ![]() ![]() | 194.1 MB 194.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8jq9MC ![]() 8jqbC ![]() 8jqcC ![]() 8wy4C ![]() 8wy5C ![]() 8x51C ![]() 8x5iC ![]() 8x5nC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_36541_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36541_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : GajA
Entire | Name: GajA |
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Components |
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-Supramolecule #1: GajA
Supramolecule | Name: GajA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 276 KDa |
-Macromolecule #1: Endonuclease GajA
Macromolecule | Name: Endonuclease GajA / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 67.079469 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MKFSNITIKN FRNFEKVNIN LDNKNVIFGM NDIGKTNFLY ALRFLLDKEI RKFGFNKSDY HKHDTSKKIE IILTLDLSNY EKDEDTKKL ISVVKGARTS ANADVFYIAL ESKYDDKELY GNIILKWGSE LDNLIDIPGR GNINALDNVF KVIYINPLVD L DKLFAQNK ...String: MKFSNITIKN FRNFEKVNIN LDNKNVIFGM NDIGKTNFLY ALRFLLDKEI RKFGFNKSDY HKHDTSKKIE IILTLDLSNY EKDEDTKKL ISVVKGARTS ANADVFYIAL ESKYDDKELY GNIILKWGSE LDNLIDIPGR GNINALDNVF KVIYINPLVD L DKLFAQNK KYIFEESQGN ESDEGILNNI KSLTDQVNQQ IGEMTIIKGF QQEITSEYRS LKKEEVSIEL KSEMAIKGFF SD IIPYIKK DGDSNYYPTS GDGRRKMLSY SIYNYLAKKK YEDKIVIYLI EEPEISLHRS MQIALSKQLF EQSTYKYFFL STH SPELLY EMDNTRLIRV HSTEKVVCSS HMYNVEEAYG SVKKKLNKAL SSALFAERVL LIEGPSEKIL FEKVLDEVEP EYEL NGGFL LEVGGTYFNH YVCTLNDLGI THIIKTDNDL KSKKGKKGVY ELLGLNRCLN LLGRENLDEI TIDIPEDIKG KKKKE RLNE RKKEIFKQYK NEVGEFLGER IYLSEIDLEN DLYSAIGESM KRIFENEDPV HYLQKSKLFN MVELVNNLST KDCFDV FEH EKFACLKELV GSDRG UniProtKB: Endonuclease GajA |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 8 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.6 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3023069 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-8jq9: |