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- EMDB-38071: Tetramer Gabija with ATP -

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Basic information

Entry
Database: EMDB / ID: EMD-38071
TitleTetramer Gabija with ATP
Map data
Sample
  • Complex: GajA tetramer with four GajB(ATP binding state)
    • Protein or peptide: Endonuclease GajA
    • Protein or peptide: Gabija protein GajB
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsAnti-Phage System / IMMUNE SYSTEM / DNA BINDING PROTEIN
Function / homology
Function and homology information


DNA helicase activity / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / 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 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 VD045 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 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
DepositionNov 17, 2023-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38071.png

Downloads & links

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Map

FileDownload / File: emd_38071.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.84 Å
Density
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.0333656 - 1.5812799
Average (Standard dev.)0.0011057961 (±0.027959082)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 322.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38071_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_38071_half_map_2.map
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 tetramer with four GajB(ATP binding state)

EntireName: GajA tetramer with four GajB(ATP binding state)
Components
  • Complex: GajA tetramer with four GajB(ATP binding state)
    • Protein or peptide: Endonuclease GajA
    • Protein or peptide: Gabija protein GajB
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: GajA tetramer with four GajB(ATP binding state)

SupramoleculeName: GajA tetramer with four GajB(ATP binding state) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Bacillus cereus VD045 (bacteria)

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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 VD045 (bacteria)
Molecular weightTheoretical: 67.079469 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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: 4 / Enantiomer: LEVO
Source (natural)Organism: Bacillus cereus VD045 (bacteria)
Molecular weightTheoretical: 57.757656 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.6 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 190783

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