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- PDB-8qyc: Zorya anti-bacteriophage defense system ZorD in complex with ATP-... -

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Entry
Database: PDB / ID: 8qyc
TitleZorya anti-bacteriophage defense system ZorD in complex with ATP-gamma-S
ComponentsDEAD/DEAH box helicase
KeywordsANTIVIRAL PROTEIN / Nuclease
Function / homologyPHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsHu, H. / Taylor, N.M.I.
Funding support Denmark, 3items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF17OC0031006 Denmark
Novo Nordisk FoundationNNF21OC0071948 Denmark
LundbeckfondenR347-2020-2429 Denmark
CitationJournal: Nature / Year: 2025
Title: Structure and mechanism of the Zorya anti-phage defence system.
Authors: Haidai Hu / Philipp F Popp / Thomas C D Hughes / Aritz Roa-Eguiara / Nicole R Rutbeek / Freddie J O Martin / Ivo Alexander Hendriks / Leighton J Payne / Yumeng Yan / Dorentina Humolli / ...Authors: Haidai Hu / Philipp F Popp / Thomas C D Hughes / Aritz Roa-Eguiara / Nicole R Rutbeek / Freddie J O Martin / Ivo Alexander Hendriks / Leighton J Payne / Yumeng Yan / Dorentina Humolli / Victor Klein-Sousa / Inga Songailiene / Yong Wang / Michael Lund Nielsen / Richard M Berry / Alexander Harms / Marc Erhardt / Simon A Jackson / Nicholas M I Taylor /
Abstract: Zorya is a recently identified and widely distributed bacterial immune system that protects bacteria from viral (phage) infections. Three Zorya subtypes have been identified, each containing ...Zorya is a recently identified and widely distributed bacterial immune system that protects bacteria from viral (phage) infections. Three Zorya subtypes have been identified, each containing predicted membrane-embedded ZorA-ZorB (ZorAB) complexes paired with soluble subunits that differ among Zorya subtypes, notably ZorC and ZorD in type I Zorya systems. Here we investigate the molecular basis of Zorya defence using cryo-electron microscopy, mutagenesis, fluorescence microscopy, proteomics and functional studies. We present cryo-electron microscopy structures of ZorAB and show that it shares stoichiometry and features of other 5:2 inner membrane ion-driven rotary motors. The ZorAB complex contains a dimeric ZorB peptidoglycan-binding domain and a pentameric α-helical coiled-coil tail made of ZorA that projects approximately 70 nm into the cytoplasm. We also characterize the structure and function of the soluble Zorya components ZorC and ZorD, finding that they have DNA-binding and nuclease activity, respectively. Comprehensive functional and mutational analyses demonstrate that all Zorya components work in concert to protect bacterial cells against invading phages. We provide evidence that ZorAB operates as a proton-driven motor that becomes activated after sensing of phage invasion. Subsequently, ZorAB transfers the phage invasion signal through the ZorA cytoplasmic tail to recruit and activate the soluble ZorC and ZorD effectors, which facilitate the degradation of the phage DNA. In summary, our study elucidates the foundational mechanisms of Zorya function as an anti-phage defence system.
History
DepositionOct 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DEAD/DEAH box helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,4032
Polymers122,8801
Non-polymers5231
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein DEAD/DEAH box helicase


Mass: 122880.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: BF481_003650 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0V7WZM1
#2: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
Has ligand of interestY
Has protein modificationN

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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: Zorya anti-bacteriophage defense system ZorD in complex with ATP-gamma-S
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 211477 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0027368
ELECTRON MICROSCOPYf_angle_d0.42210026
ELECTRON MICROSCOPYf_dihedral_angle_d11.0772743
ELECTRON MICROSCOPYf_chiral_restr0.041123
ELECTRON MICROSCOPYf_plane_restr0.0041295

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