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- EMDB-43563: Cryo-EM structure of a type I ZorAB complex from Shewanella sp. s... -

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Basic information

Entry
Database: EMDB / ID: EMD-43563
TitleCryo-EM structure of a type I ZorAB complex from Shewanella sp. strain ANA-3, composite map
Map datacomposite map generated from sharpened consensus and local refinement of peptidoglycan-binding domain
Sample
  • Complex: ZorAB complex
    • Protein or peptide: Chemotaxis protein MotB-related protein
    • Protein or peptide: MotA/TolQ/ExbB proton channel domain-containing protein
  • Ligand: SODIUM ION
  • Ligand: water
Keywordsphage defense / zorya / phage / membrane protein complex / MEMBRANE PROTEIN
Function / homology: / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain / membrane / MotA/TolQ/ExbB proton channel domain-containing protein / Chemotaxis protein MotB-related protein
Function and homology information
Biological speciesShewanella sp. ANA-3 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsDeme JC / Lea SM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CCR Core Funding for Lea Group United States
CitationJournal: Nat Commun / Year: 2025
Title: Modularity of Zorya defense systems during phage inhibition.
Authors: Giuseppina Mariano / Justin C Deme / Jennifer J Readshaw / Matthew J Grobbelaar / Mackenzie Keenan / Yasmin El-Masri / Lindsay Bamford / Suraj Songra / Tim R Blower / Tracy Palmer / Susan M Lea /
Abstract: Bacteria have evolved an extraordinary diversity of defense systems against bacteriophage (phage) predation. However, the molecular mechanisms underlying these anti-phage systems often remain elusive. ...Bacteria have evolved an extraordinary diversity of defense systems against bacteriophage (phage) predation. However, the molecular mechanisms underlying these anti-phage systems often remain elusive. Here, we provide mechanistic and structural insights into Zorya phage defense systems. Using cryo-EM structural analyses, we show that the Zorya type I and II core components, ZorA and ZorB, assemble in a 5:2 complex that is similar to inner-membrane ion-driven, rotary motors that power flagellar rotation, type 9 secretion, gliding and the Ton nutrient uptake systems. The ZorAB complex has an elongated cytoplasmic tail assembled by bundling the C-termini of the five ZorA subunits. Mutagenesis demonstrates that peptidoglycan binding by the periplasmic domains of ZorB, the structured cytoplasmic tail of ZorA, and ion flow through the motor is important for function in both type I and II systems. Furthermore, we identify ZorE as the effector module of the Zorya II system, possessing nickase activity. Our work reveals the molecular basis of the activity of Zorya systems and highlights the ZorE nickase as crucial for population-wide immunity in the type II system.
History
DepositionJan 31, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43563.png

Downloads & links

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Map

FileDownload / File: emd_43563.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map generated from sharpened consensus and local refinement of peptidoglycan-binding domain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.72 Å/pix.
x 480 pix.
= 347.04 Å		0.72 Å/pix.
x 480 pix.
= 347.04 Å		0.72 Å/pix.
x 480 pix.
= 347.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.723 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.8
Minimum - Maximum-45.718580000000003 - 76.768249999999995
Average (Standard dev.)-0.00011682914 (±1.0612363)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 347.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: composite map generated from unsharpened consensus and local...

Fileemd_43563_additional_1.map
Annotationcomposite map generated from unsharpened consensus and local refinement of peptidoglycan-binding domain
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ZorAB complex

EntireName: ZorAB complex
Components
  • Complex: ZorAB complex
    • Protein or peptide: Chemotaxis protein MotB-related protein
    • Protein or peptide: MotA/TolQ/ExbB proton channel domain-containing protein
  • Ligand: SODIUM ION
  • Ligand: water

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Supramolecule #1: ZorAB complex

SupramoleculeName: ZorAB complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Shewanella sp. ANA-3 (bacteria)

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Macromolecule #1: Chemotaxis protein MotB-related protein

MacromoleculeName: Chemotaxis protein MotB-related protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Shewanella sp. ANA-3 (bacteria)
Molecular weightTheoretical: 32.12708 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDRLFTRGST KVDEENPYWM SFSDLMSGLL VIFILAAVAL IIELTQKSEQ IDASIEELKK AEEARRNILI DIKEELAKQN IHVEIVEND TVLRIPESTL SFESGKDTLP ENTTVKNEVR LIGIALHKAI TTNERWKYLD TVFVEGHTDS NGIWYRGKGN W GLSTDRAV ...String:
MDRLFTRGST KVDEENPYWM SFSDLMSGLL VIFILAAVAL IIELTQKSEQ IDASIEELKK AEEARRNILI DIKEELAKQN IHVEIVEND TVLRIPESTL SFESGKDTLP ENTTVKNEVR LIGIALHKAI TTNERWKYLD TVFVEGHTDS NGIWYRGKGN W GLSTDRAV SIWKLWQTEI NVAPKLSVLT NYNGQLLFSV SGYADTRRVD LQETTEEQRA RNRRIDIRFT VKKPKIEDYE KA KNVENLY FQGQFGSWSH PQFEKGGGSG GGSGGGSWSH PQFEK

UniProtKB: Chemotaxis protein MotB-related protein

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Macromolecule #2: MotA/TolQ/ExbB proton channel domain-containing protein

MacromoleculeName: MotA/TolQ/ExbB proton channel domain-containing protein
type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Shewanella sp. ANA-3 (bacteria)
Molecular weightTheoretical: 77.102953 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MATERQIELS WLLPDFSHLS FHPQTGTALS SLFVAITLTV TLLFIAYLLY KSIDVVLKIN WLQKALEPLE RKDVAQKKEV LYQLAKSKS KGKSKGIGFL WMEFDETLVE VRKGDQIEIR NTLDAGHFFN TYTLANSVTE NRLIAAVPGF LTALGVIGTF M GLQLGLAD ...String:
MATERQIELS WLLPDFSHLS FHPQTGTALS SLFVAITLTV TLLFIAYLLY KSIDVVLKIN WLQKALEPLE RKDVAQKKEV LYQLAKSKS KGKSKGIGFL WMEFDETLVE VRKGDQIEIR NTLDAGHFFN TYTLANSVTE NRLIAAVPGF LTALGVIGTF M GLQLGLAD LKLGAGVDVT TMQDGVAGVV NGAKIAFLTS VWGVALSVFF NFFEKLCEQF IRSKIRELED KVDFLFPRVR PE EQLQIIS ENSSESRNVL QGLAEKIGEK MQEAMVTATQ GIQSSLESSL SKIMAPAINK LVDETSQGNQ KALEGLLESF MDR FGQAGN LQRSALDDVS NKVNQSVEAM QLTMSNFVEQ LQKSQAESGD REKALIADIS HQVSKLSSQS EDIHQKLTSY VENQ IGKIS SQMQIREEAS AKRDSELVNV IGQQVNELVN NSRRQGELLT SFVETQLNNL TKSFDERDKR STELETTRNN KIEKQ TEAI VKISNELIST VEKSVSEQLA AVKHLVSQGE TLQNSVNASV EAAAQATQAM KESSIELRVS ADHMRVLSSH VNDAGN KLS GAIKSAVDST ADLANQNQIS AQRIENARES LMKDVSRFSE LSDQIKALIT SASSTFTELK STQRDFIGNL KEEVESL SR KMTDMLEEYS QQANGQTAEH LKIWSQSVTD YSTQMNSAVK ALSSVVDEMQ VKLG

UniProtKB: MotA/TolQ/ExbB proton channel domain-containing protein

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Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 140 / 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / 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: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 587313
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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