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- EMDB-36569: Structure of Gabija GajA-GajB 4:1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-36569
TitleStructure of Gabija GajA-GajB 4:1 complex
Map data
Sample
  • Complex: 4:1 GajAB complex
    • Protein or peptide: Endonuclease GajA
    • Protein or peptide: Gabija protein GajB
KeywordsAnti-phage / IMMUNE 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 helicase, ATP-binding domain / UvrD-like DNA helicase ATP-binding domain profile. ...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 helicase, ATP-binding domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Endonuclease GajA / Gabija protein GajB
Similarity search - Component
Biological speciesBacillus cereus (strain VD045) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsLi J / Wang Z / Wang L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: 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
DepositionJun 13, 2023-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36569.png

Downloads & links

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Map

FileDownload / File: emd_36569.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 380 pix.
= 319.2 Å		0.84 Å/pix.
x 380 pix.
= 319.2 Å		0.84 Å/pix.
x 380 pix.
= 319.2 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.3853403 - 0.6805293
Average (Standard dev.)0.00016373511 (±0.020000845)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 319.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36569_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36569_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : 4:1 GajAB complex

EntireName: 4:1 GajAB complex
Components
  • Complex: 4:1 GajAB complex
    • Protein or peptide: Endonuclease GajA
    • Protein or peptide: Gabija protein GajB

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Supramolecule #1: 4:1 GajAB complex

SupramoleculeName: 4:1 GajAB complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus cereus (strain VD045) (bacteria)
Molecular weightTheoretical: 335 KDa

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Macromolecule #1: Endonuclease GajA

MacromoleculeName: Endonuclease GajA / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Bacillus cereus (strain VD045) (bacteria)
Molecular weightTheoretical: 67.079469 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: Gabija protein GajB

MacromoleculeName: Gabija protein GajB / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus cereus (strain VD045) (bacteria)
Molecular weightTheoretical: 57.757656 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIEDEMSREQ IIKDGGNILV TAGAGSGKTT ILVSKIEADL KENKTHYSIA AVTFTNKAAK EIEGRLGYSS RGNFIGTNDG FVESEIIRP FIKDAFGNDY PDNFTAEYFD NQFASYDKGL QVLKYQNILG TYSNPKKNFK FQLALDILKK SLVARQYIFS K YFKIFIDE ...String:
MIEDEMSREQ IIKDGGNILV TAGAGSGKTT ILVSKIEADL KENKTHYSIA AVTFTNKAAK EIEGRLGYSS RGNFIGTNDG FVESEIIRP FIKDAFGNDY PDNFTAEYFD NQFASYDKGL QVLKYQNILG TYSNPKKNFK FQLALDILKK SLVARQYIFS K YFKIFIDE YQDSDKDMHN LFMYLKDQLK IKLFIVGDPK QSIYIWRGAE PENFNGLIEN STDFNKYHLT SNFRCCQDIQ NY SNLFNEE TRSLIKEKNE VQNVISIADD MPISDILLKL TEEKQVLNIE AELVILVRRR NQAIEIMKEL NEEGFNFIFI PQT PLDRAT PNATLLKEVI KYVKNDRYSI YDLAAEIVGN LSSREIKEIQ KIINELLVPN INQVLINQVL INLFAKLEIT LDTR EITAF TEVMMTNEFD IAFDTNEYLH KIFTVHSAKG LEFNQVIITA SDYNVHYNRD TNEHYVATTR AKDKLIVIMD NKKYS DYIE TLMKELKIKN IIKSI

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

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4218276
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8jqc:
Structure of Gabija GajA-GajB 4:1 complex

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