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Structure paper

TitleStructure and mechanism of the Zorya anti-phage defence system.
Journal, issue, pagesNature, Vol. 639, Issue 8056, Page 1093-1101, Year 2025
Publish dateDec 11, 2024
AuthorsHaidai 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 /
PubMed AbstractZorya 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.
External linksNature / PubMed:39662505 / PubMed Central
MethodsEM (single particle)
Resolution2.07 - 3.6 Å
Structure data

18747

8qy7

EMDB-18747, PDB-8qy7:
Zorya anti-bacteriophage defense system ZorD apo form
Method: EM (single particle) / Resolution: 2.66 Å

18750

8qyc

EMDB-18750, PDB-8qyc:
Zorya anti-bacteriophage defense system ZorD in complex with ATP-gamma-S
Method: EM (single particle) / Resolution: 2.75 Å

18751

8qyd

EMDB-18751, PDB-8qyd:
Zorya anti-bacteriophage defense system ZorAB
Method: EM (single particle) / Resolution: 2.67 Å

18754

8qyh

EMDB-18754, PDB-8qyh:
Zorya anti-bacteriophage defense system ZorAB ZorA E86A_E89A, Calcium binding site mutation
Method: EM (single particle) / Resolution: 2.4 Å

18756

8qyk

EMDB-18756, PDB-8qyk:
Zorya anti-bacteriophage defense system ZorAB, ZorA delta_359-592, ZorA tail middle deletion.
Method: EM (single particle) / Resolution: 2.07 Å

18766

8qyy

EMDB-18766, PDB-8qyy:
Zorya anti-bacteriophage defense system ZorAB, ZorA delta_435-729, ZorA tail tip deletion.
Method: EM (single particle) / Resolution: 2.56 Å

18948

8r68

EMDB-18948, PDB-8r68:
Zorya anti-bacteriophage defense system ZorC WT
Method: EM (single particle) / Resolution: 3.6 Å

Chemicals

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

ChemComp-CA:
Unknown entry

ChemComp-PEE:
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipid*YM

ChemComp-PLM:
PALMITIC ACID

ChemComp-HOH:
WATER

Source
  • escherichia coli (E. coli)
KeywordsANTIVIRAL PROTEIN / Nuclease / membrane protein

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