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- PDB-8vvn: Cryo-EM structure of a type I ZorAB complex from Shewanella sp. s... -

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Basic information

Entry
Database: PDB / ID: 8vvn
TitleCryo-EM structure of a type I ZorAB complex from Shewanella sp. strain ANA-3
Components
  • Chemotaxis protein MotB-related protein
  • MotA/TolQ/ExbB proton channel domain-containing protein
KeywordsMEMBRANE PROTEIN / phage defense / zorya / phage / membrane protein complex
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsDeme, J.C. / Lea, S.M.
Funding support United States, 1items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Chemotaxis protein MotB-related protein
A: Chemotaxis protein MotB-related protein
C: MotA/TolQ/ExbB proton channel domain-containing protein
D: MotA/TolQ/ExbB proton channel domain-containing protein
E: MotA/TolQ/ExbB proton channel domain-containing protein
F: MotA/TolQ/ExbB proton channel domain-containing protein
G: MotA/TolQ/ExbB proton channel domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)449,8159
Polymers449,7697
Non-polymers462
Water2,522140
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 Chemotaxis protein MotB-related protein


Mass: 32127.080 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella sp. ANA-3 (bacteria) / Gene: Shewana3_3786 / Production host: Escherichia coli (E. coli) / References: UniProt: A0L1T5
#2: Protein
MotA/TolQ/ExbB proton channel domain-containing protein


Mass: 77102.953 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella sp. ANA-3 (bacteria) / Gene: Shewana3_3785 / Production host: Escherichia coli (E. coli) / References: UniProt: A0L1T4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
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: ZorAB complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Shewanella sp. ANA-3 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 54 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 587313 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00413037
ELECTRON MICROSCOPYf_angle_d0.58617641
ELECTRON MICROSCOPYf_dihedral_angle_d4.6441696
ELECTRON MICROSCOPYf_chiral_restr0.0422067
ELECTRON MICROSCOPYf_plane_restr0.0042199

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