+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35977 | |||||||||
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Title | GajA-GajB complex | |||||||||
Map data | GajA-GajB complex | |||||||||
Sample |
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Keywords | Complex / DNA-binding / Immunity system / DNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information DNA helicase complex / recombinational repair / 3'-5' DNA helicase activity / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / hydrolase activity / DNA binding / ATP binding / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Bacillus cereus (strain VD045) (bacteria) / Bacillus cereus VD045 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Wei T / Ma J / Huo Y | |||||||||
Funding support | 1 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structural and biochemical insights into the mechanism of the Gabija bacterial immunity system. Authors: Yanwu Huo / Lingfei Kong / Ye Zhang / Min Xiao / Kang Du / Sunyuntao Xu / Xiaoxue Yan / Jun Ma / Taotao Wei / Abstract: The Gabija system is a newly discovered bacterial immune system that consists of GajA and GajB. Here we report the cryo-EM structure of the Gabija complex from Bacillus cereus VD045 at 3.6 Å, ...The Gabija system is a newly discovered bacterial immune system that consists of GajA and GajB. Here we report the cryo-EM structure of the Gabija complex from Bacillus cereus VD045 at 3.6 Å, which provides the direct evidence of interactions between GajA and GajB. The Gabija complex is an octameric ring structure with four GajA and four GajB. GajA is an OLD nucleases family protein, while GajB belongs to the SF1 helicases. The Gabija complex has sequence-specific DNA nuclease activity and prefers circular rather than linear DNA as substrate, its activity is more sensitive to concentrations change of nucleotides compared to GajA alone. Our data suggest a mechanism of Gabija immunity: the nuclease activity of Gabija complex is inhibited under physiological conditions, while it is activated by depletion of NTP and dNTP upon the replication and transcription of invading phages and cleave the circular DNA to prevent phage DNA replication. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35977.map.gz | 49.3 MB | EMDB map data format | |
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Header (meta data) | emd-35977-v30.xml emd-35977.xml | 15.3 KB 15.3 KB | Display Display | EMDB header |
Images | emd_35977.png | 117.8 KB | ||
Filedesc metadata | emd-35977.cif.gz | 5.9 KB | ||
Others | emd_35977_half_map_1.map.gz emd_35977_half_map_2.map.gz | 39.4 MB 39.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35977 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35977 | HTTPS FTP |
-Validation report
Summary document | emd_35977_validation.pdf.gz | 815.8 KB | Display | EMDB validaton report |
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Full document | emd_35977_full_validation.pdf.gz | 815.4 KB | Display | |
Data in XML | emd_35977_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | emd_35977_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35977 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35977 | HTTPS FTP |
-Related structure data
Related structure data | 8j4tMC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_35977.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | GajA-GajB complex | ||||||||||||||||||||
Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map 1 for GajA-GajB complex
File | emd_35977_half_map_1.map | ||||||||||||
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Annotation | Half map 1 for GajA-GajB complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2 for GajA-GajB complex
File | emd_35977_half_map_2.map | ||||||||||||
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Annotation | Half map 2 for GajA-GajB complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : GajA-GajB complex
Entire | Name: GajA-GajB complex |
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Components |
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-Supramolecule #1: GajA-GajB complex
Supramolecule | Name: GajA-GajB complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Bacillus cereus (strain VD045) (bacteria) |
Molecular weight | Theoretical: 500 KDa |
-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: 69.275961 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MASWSHPQEK GALEVLFQGP MKFSNITIKN FRNFEKVNIN LDNKNVIFGM NDIGKTNFLY ALRFLLDKEI RKFGFNKSDY HKHDTSKKI EIILTLDLSN YEKDEDTKKL ISVVKGARTS ANADVFYIAL ESKYDDKELY GNIILKWGSE LDNLIDIPGR G NINALDNV ...String: MASWSHPQEK GALEVLFQGP MKFSNITIKN FRNFEKVNIN LDNKNVIFGM NDIGKTNFLY ALRFLLDKEI RKFGFNKSDY HKHDTSKKI EIILTLDLSN YEKDEDTKKL ISVVKGARTS ANADVFYIAL ESKYDDKELY GNIILKWGSE LDNLIDIPGR G NINALDNV FKVIYINPLV DLDKLFAQNK KYIFEESQGN ESDEGILNNI KSLTDQVNQQ IGEMTIIKGF QQEITSEYRS LK KEEVSIE LKSEMAIKGF FSDIIPYIKK DGDSNYYPTS GDGRRKMLSY SIYNYLAKKK YEDKIVIYLI EEPEISLHRS MQI ALSKQL FEQSTYKYFF LSTHSPELLY EMDNTRLIRV HSTEKVVCSS HMYNVEEAYG SVKKKLNKAL SSALFAERVL LIEG PSEKI LFEKVLDEVE PEYELNGGFL LEVGGTYFNH YVCTLNDLGI THIIKTDNDL KSKKGKKGVY ELLGLNRCLN LLGRE NLDE ITIDIPEDIK GKKKKERLNE RKKEIFKQYK NEVGEFLGER IYLSEIDLEN DLYSAIGESM KRIFENEDPV HYLQKS KLF NMVELVNNLS TKDCFDVFEH EKFACLKELV GSDRG UniProtKB: Endonuclease GajA |
-Macromolecule #2: Gabija protein GajB
Macromolecule | Name: Gabija protein GajB / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus cereus VD045 (bacteria) |
Molecular weight | Theoretical: 57.139992 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MSREQIIKDG GNILVTAGAG SGKTTILVSK IEADLKENKT HYSIAAVTFT NKAAKEIEGR LGYSSRGNFI GTNDGFVESE IIRPFIKDA FGNDYPDNFT AEYFDNQFAS YDKGLQVLKY QNILGTYSNP KKNFKFQLAL DILKKSLVAR QYIFSKYFKI F IDEYQDSD ...String: MSREQIIKDG GNILVTAGAG SGKTTILVSK IEADLKENKT HYSIAAVTFT NKAAKEIEGR LGYSSRGNFI GTNDGFVESE IIRPFIKDA FGNDYPDNFT AEYFDNQFAS YDKGLQVLKY QNILGTYSNP KKNFKFQLAL DILKKSLVAR QYIFSKYFKI F IDEYQDSD KDMHNLFMYL KDQLKIKLFI VGDPKQSIYI WRGAEPENFN GLIENSTDFN KYHLTSNFRC CQDIQNYSNL FN EETRSLI KEKNEVQNVI SIADDMPISD ILLKLTEEKQ VLNIEAELVI LVRRRNQAIE IMKELNEEGF NFIFIPQTPL DRA TPNATL LKEVIKYVKN DRYSIYDLAA EIVGNLSSRE IKEIQKIINE LLVPNINQVL INQVLINLFA KLEITLDTRE ITAF TEVMM TNEFDIAFDT NEYLHKIFTV HSAKGLEFNQ VIITASDYNV HYNRDTNEHY VATTRAKDKL IVIMDNKKYS DYIET LMKE LKIKNIIKSI UniProtKB: Gabija protein GajB |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 279580 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |