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- EMDB-18751: Zorya anti-bacteriophage defense system ZorAB -

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Basic information

Entry
Database: EMDB / ID: EMD-18751
TitleZorya anti-bacteriophage defense system ZorAB
Map data
Sample
  • Organelle or cellular component: Zorya anti-bacteriophage defense system ZorAB
    • Protein or peptide: Anti-phage defense ZorAB system ZorA
    • Protein or peptide: Membrane protein
  • Ligand: CARDIOLIPIN
  • Ligand: CALCIUM ION
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: PALMITIC ACID
  • Ligand: water
KeywordsNuclease / ANTIVIRAL PROTEIN
Function / homology: / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.67 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-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18751.png

Downloads & links

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Map

FileDownload / File: emd_18751.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 500 pix.
= 416. Å		0.83 Å/pix.
x 500 pix.
= 416. Å		0.83 Å/pix.
x 500 pix.
= 416. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-2.414227 - 4.1398907
Average (Standard dev.)-0.00012386891 (±0.06777438)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 416.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_18751_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18751_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 : Zorya anti-bacteriophage defense system ZorAB

EntireName: Zorya anti-bacteriophage defense system ZorAB
Components
  • Organelle or cellular component: Zorya anti-bacteriophage defense system ZorAB
    • Protein or peptide: Anti-phage defense ZorAB system ZorA
    • Protein or peptide: Membrane protein
  • Ligand: CARDIOLIPIN
  • Ligand: CALCIUM ION
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: PALMITIC ACID
  • Ligand: water

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Supramolecule #1: Zorya anti-bacteriophage defense system ZorAB

SupramoleculeName: Zorya anti-bacteriophage defense system ZorAB / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Anti-phage defense ZorAB system ZorA

MacromoleculeName: Anti-phage defense ZorAB system ZorA / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 80.339195 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSWLNSILVT LTSVEPYKVP VTVIVTVTFA FVCFIFFYLL RSIRIIYGLK KYTRSINSIE KSAPEVQLEH LKSLFQRSEL KHAWNEFEE SLHSQYELEN GEEKIVRIRA TAPSASFFSE QQLVDIPLNT EFFKHLPGIL TGMGIIGTFY GLMIGLNHFD P STPEQVSS ...String:
MSWLNSILVT LTSVEPYKVP VTVIVTVTFA FVCFIFFYLL RSIRIIYGLK KYTRSINSIE KSAPEVQLEH LKSLFQRSEL KHAWNEFEE SLHSQYELEN GEEKIVRIRA TAPSASFFSE QQLVDIPLNT EFFKHLPGIL TGMGIIGTFY GLMIGLNHFD P STPEQVSS SVNNLLRDVL YAFLGSAFAI FASILVTWLE KLSIAKSYKY LEKFTAALDS LYDSGVGEEY LASLVKSSNE SA TQARHLK ESLVTDLRDM LLHLAESQKI ENERLANTLS ATYRESGSQF ADQVSGAIEN SLKSPLDKIA GAVQTASGDQ SGM VQNMLQ NVLTAFMAKL DTTFGQQFTN LNEMMGQTVG AIQTMQTGFS ALLQDMRQVS DDSRQGSAQL IEQLLSEMKS GQQA LQAGM NDMLTSLQVS VAKIGAEGEG AGERIARQLE KMFADSEARE KAQAEHMAAF VEAIQNSVQQ GQSATMEKMA ASVGA LGEQ LGSLFGQIDK GQQQISATQQ ANQQSLHEQT QRVMSEVDDQ IKQLVETVAS QHQGTTETLR LLAEQTNRQI QDMQAG ADK MRLAAERFEH AGERVSEANH LTADVLNKAQ SAGSSLSLAT SELTSVVADY RNNREAVSKS IAMLELLAAN TQSEQTT RN QFIADLKQHG ERLQSYNREA QVFMENVSDV LGKGFEDFSE GVSRSLDKTL GKLDVEMAKA SNLLAGSVEQ LGESVSEL D DVLSRVRT

UniProtKB: UNIPROTKB: A0A0V7WZR2

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Macromolecule #2: Membrane protein

MacromoleculeName: Membrane protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 28.103229 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFGNAFGVKK RRSDEAEKPF WISYADLMTA MMVLFLVVMV ASLSSVTQRI QRAEQGEKAR GQDISRLCER LELHARNVNK NIVVDCHDN RISFGEAGRF AHNQFFLNAE GQKALQDVVP LVLEASNSEE GKKWFKQIVI EGFTDTDGSY LYNLHLSLQR S EWVMCSLL ...String:
MFGNAFGVKK RRSDEAEKPF WISYADLMTA MMVLFLVVMV ASLSSVTQRI QRAEQGEKAR GQDISRLCER LELHARNVNK NIVVDCHDN RISFGEAGRF AHNQFFLNAE GQKALQDVVP LVLEASNSEE GKKWFKQIVI EGFTDTDGSY LYNLHLSLQR S EWVMCSLL DSRSPLQKNI SAEQQLQIRK LFLAGGVSFN NAKESKEASR RVELRMQFFG LKDKRDKADE VDFPPVVNKE VC QLVMPL

UniProtKB: UNIPROTKB: A0A0V7WZP0

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Macromolecule #3: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 3 / Number of copies: 5 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 5 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #5: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 5 / Number of copies: 5 / Formula: PEE
Molecular weightTheoretical: 744.034 Da
Chemical component information

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

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Macromolecule #6: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 6 / Number of copies: 1 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 313 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 227728
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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