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- EMDB-35977: GajA-GajB complex -

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Basic information

Entry
Database: EMDB / ID: EMD-35977
TitleGajA-GajB complex
Map dataGajA-GajB complex
Sample
  • Complex: GajA-GajB complex
    • Protein or peptide: Endonuclease GajA
    • Protein or peptide: Gabija protein GajB
KeywordsComplex / DNA-binding / Immunity system / DNA BINDING PROTEIN
Function / homology
Function and homology information


recombinational repair / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / hydrolase activity / DNA binding ...recombinational repair / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / hydrolase activity / DNA binding / ATP binding / metal ion binding
Similarity search - Function
: / Overcoming lysogenization defect protein-like, TOPRIM domain / OLD protein-like, TOPRIM domain / AAA domain, group 15 / 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 ...: / Overcoming lysogenization defect protein-like, TOPRIM domain / OLD protein-like, TOPRIM domain / AAA domain, group 15 / 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 (strain VD045) (bacteria) / Bacillus cereus VD045 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsWei T / Ma J / Huo Y
Funding support1 items
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, 2023-
Header (metadata) releaseFeb 21, 2024-
Map releaseFeb 21, 2024-
UpdateFeb 21, 2024-
Current statusFeb 21, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35977.png

Downloads & links

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Map

FileDownload / File: emd_35977.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGajA-GajB complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 240 pix.
= 240. Å		1 Å/pix.
x 240 pix.
= 240. Å		1 Å/pix.
x 240 pix.
= 240. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.07362113 - 0.11017092
Average (Standard dev.)0.00013694889 (±0.003986978)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-120-120-120
Dimensions240240240
Spacing240240240
CellA=B=C: 240.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1 for GajA-GajB complex

Fileemd_35977_half_map_1.map
AnnotationHalf map 1 for GajA-GajB complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 for GajA-GajB complex

Fileemd_35977_half_map_2.map
AnnotationHalf map 2 for GajA-GajB complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GajA-GajB complex

EntireName: GajA-GajB complex
Components
  • Complex: GajA-GajB complex
    • Protein or peptide: Endonuclease GajA
    • Protein or peptide: Gabija protein GajB

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Supramolecule #1: GajA-GajB complex

SupramoleculeName: GajA-GajB complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus cereus (strain VD045) (bacteria)
Molecular weightTheoretical: 500 KDa

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Macromolecule #1: Endonuclease GajA

MacromoleculeName: Endonuclease GajA / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bacillus cereus VD045 (bacteria)
Molecular weightTheoretical: 69.275961 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Macromolecule #2: Gabija protein GajB

MacromoleculeName: Gabija protein GajB / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bacillus cereus VD045 (bacteria)
Molecular weightTheoretical: 57.139992 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 279580
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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