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- EMDB-18750: Zorya anti-bacteriophage defense system ZorD in complex with ATP-... -

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Basic information

Entry
Database: EMDB / ID: EMD-18750
TitleZorya anti-bacteriophage defense system ZorD in complex with ATP-gamma-S
Map data
Sample
  • Organelle or cellular component: Zorya anti-bacteriophage defense system ZorD in complex with ATP-gamma-S
    • Protein or peptide: DEAD/DEAH box helicase
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
KeywordsNuclease / ANTIVIRAL PROTEIN
Function / homology:
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsHu H / Taylor NMI
Funding support Denmark, 3 items
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, 2023-
Header (metadata) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18750.png

Downloads & links

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Map

FileDownload / File: emd_18750.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 332.8 Å		0.83 Å/pix.
x 400 pix.
= 332.8 Å		0.83 Å/pix.
x 400 pix.
= 332.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-4.6689205 - 6.6181097
Average (Standard dev.)-0.00015477187 (±0.109504)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 332.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_18750_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_18750_half_map_2.map
Projections & Slices
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Sample components

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Entire : Zorya anti-bacteriophage defense system ZorD in complex with ATP-...

EntireName: Zorya anti-bacteriophage defense system ZorD in complex with ATP-gamma-S
Components
  • Organelle or cellular component: Zorya anti-bacteriophage defense system ZorD in complex with ATP-gamma-S
    • Protein or peptide: DEAD/DEAH box helicase
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

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Supramolecule #1: Zorya anti-bacteriophage defense system ZorD in complex with ATP-...

SupramoleculeName: Zorya anti-bacteriophage defense system ZorD in complex with ATP-gamma-S
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: DEAD/DEAH box helicase

MacromoleculeName: DEAD/DEAH box helicase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 122.880039 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLKRLLSKLT GNRQQIEHHL KNQYQVEENG LSFPLSLVDD SQLWALASWL EQLAEEDYLI SLTDRWLLSW EALYRLLEDE EHASSLPLI GVPDILPLRA SLSSRGALSD SDFRVWIAEW ATFPARKPIR FSRTGAILTH DNQQYLLSRE NWALLQATEQ L SAQQIQTP ...String:
MLKRLLSKLT GNRQQIEHHL KNQYQVEENG LSFPLSLVDD SQLWALASWL EQLAEEDYLI SLTDRWLLSW EALYRLLEDE EHASSLPLI GVPDILPLRA SLSSRGALSD SDFRVWIAEW ATFPARKPIR FSRTGAILTH DNQQYLLSRE NWALLQATEQ L SAQQIQTP GETTNQLGWA AIRKCAKLAA AKFDDYLEKT HVIKPTSLSL RLRKATVADT AVIEIEPHFE DQPANWLGSF DK NLQVHDS YRIPGENGEL SHVIIPPEVK EVLNSIHSIP GRRVAGSEAL SFVRNPYTFL GEDAASVIAP EEHEQALFDA RIF FHHFRL IPQLNTENKI TEVTLILEPV SPVPQPEITF VFSAPWELDK FIQQLGISVA AQMPAGSWQG YELELSQFTE QQWH DCQAL LTRWQQEIEG KEFSDVLDIA KYGDRVIGIG EFEKISSPWL TKAQSENWLP DGIDFSAFSI ETLSGWQPEN PLHFD ELQE IITQAEAAGE TYITTPWNDS QLPLDAAKTF SKNWEKQQIT ANEYQGNVAD KTARAVLKIE QNIEETAYIK QRRNSL LNA RHAEPEIPLS LKEHIRLKDH QREGVAWLQQ LFLRSPEETA GCLLADDMGL GKTLQILSFL VWFIEKFPQE PPNLIVA PV SLLDNWEREL NNFFYTAGIP VLKLYGETIK AVKYPKQAIP AHLQSKGIKN LLKPGWQGEA KIILTTYETL RDQEFSLA R QPWSIMVCDE AQKIKNPAAL ITHAANAVQA RFKVACTGTP VENTLVDLWS LFDFAQPGLL GALNEFGKQY VRPIENEDG RDTERLESLR ALIEPQTLRR TKEEVARDLP QKIEVESCKQ LTLSGVQKQL YLSSVANWQQ QQALREGMQQ AGTGMLGLLH RLKLICAHP AIVNPEPRFR DNSPKLNWLL KILAEIKHTS KDKVIIFTEL RDLQRELQHA IHQNFGFRPV IINGDSSTKS Q SQNSRQRL IDDFQAQPGF GVIILSTVAV GFGVNVQKAN HVIHFTRCWN PAKEDQATDR AYRIGQTKNV YVYYPTVRDT EI TTFEETL DDLLQRRRAL ARDMLCATPD LNCADFETIL KGA

UniProtKB: UNIPROTKB: A0A0V7WZM1

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Macromolecule #2: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 2 / Number of copies: 1 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

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

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 211477
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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