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- PDB-8j4t: GajA-GajB complex -

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Basic information

Entry
Database: PDB / ID: 8j4t
TitleGajA-GajB complex
Components
  • Endonuclease GajA
  • Gabija protein GajB
KeywordsDNA BINDING PROTEIN / Complex / DNA-binding / Immunity system
Function / homology
Function and homology information


recombinational repair / 3'-5' DNA helicase activity / defense response to virus / endonuclease activity / Hydrolases; Acting on ester bonds / hydrolase activity / DNA binding / ATP binding / metal ion binding
Similarity search - Function
AAA domain, group 15 / : / Overcoming lysogenization defect protein-like, TOPRIM domain / OLD protein-like, TOPRIM domain / AAA ATPase domain / AAA domain / UvrD-like helicase C-terminal domain / UvrD-like helicase C-terminal domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type ...AAA domain, group 15 / : / Overcoming lysogenization defect protein-like, TOPRIM domain / OLD protein-like, TOPRIM domain / AAA ATPase domain / AAA domain / UvrD-like helicase C-terminal domain / UvrD-like helicase C-terminal domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type / UvrD-like helicase, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Endonuclease GajA / Gabija protein GajB
Similarity search - Component
Biological speciesBacillus cereus VD045 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsWei, T. / Ma, J. / Huo, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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
DepositionApr 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endonuclease GajA
G: Gabija protein GajB
C: Endonuclease GajA
F: Gabija protein GajB
D: Endonuclease GajA
B: Endonuclease GajA
E: Gabija protein GajB
H: Gabija protein GajB


Theoretical massNumber of molelcules
Total (without water)505,6648
Polymers505,6648
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Endonuclease GajA


Mass: 69275.961 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus VD045 (bacteria) / Gene: gajA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J8H9C1
#2: Protein
Gabija protein GajB / Putative helicase GajB


Mass: 57139.992 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus VD045 (bacteria) / Gene: gajB, IIE_04983 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J8HQ06

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: GajA-GajB complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.5 MDa / Experimental value: YES
Source (natural)Organism: Bacillus cereus (strain VD045) (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 279580 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00323256
ELECTRON MICROSCOPYf_angle_d0.50231236
ELECTRON MICROSCOPYf_dihedral_angle_d4.7433036
ELECTRON MICROSCOPYf_chiral_restr0.0413396
ELECTRON MICROSCOPYf_plane_restr0.0043992

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