+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37915 | |||||||||
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Title | GajA tetramer with ATP | |||||||||
Map data | ||||||||||
Sample |
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Keywords | endonuclease / Complex / DNA BINDING / DNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / metal ion binding Similarity search - Function | |||||||||
Biological species | Bacillus cereus VD045 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.81 Å | |||||||||
Authors | Li J / Wang Z / Wang L | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nature / Year: 2024 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 | emd_37915.map.gz | 5.6 MB | EMDB map data format | |
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Header (meta data) | emd-37915-v30.xml emd-37915.xml | 14 KB 14 KB | Display Display | EMDB header |
Images | emd_37915.png | 71.5 KB | ||
Filedesc metadata | emd-37915.cif.gz | 5.6 KB | ||
Others | emd_37915_half_map_1.map.gz emd_37915_half_map_2.map.gz | 193.9 MB 193.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37915 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37915 | HTTPS FTP |
-Related structure data
Related structure data | 8wy4MC 8jq9C 8jqbC 8jqcC 8wy5C 8x51C 8x5iC 8x5nC 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_37915.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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: #2
File | emd_37915_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37915_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : GajA tetramer with ATP
Entire | Name: GajA tetramer with ATP |
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Components |
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-Supramolecule #1: GajA tetramer with ATP
Supramolecule | Name: GajA tetramer with ATP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Bacillus cereus VD045 (bacteria) |
-Macromolecule #1: Endonuclease GajA
Macromolecule | Name: Endonuclease GajA / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus cereus VD045 (bacteria) |
Molecular weight | Theoretical: 66.750133 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
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 GS UniProtKB: Endonuclease GajA |
-Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-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: 1.8 µm / Nominal defocus min: 1.4000000000000001 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.25 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 56959 |