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- PDB-9zn5: Hybrid model of a dimer of BrxC-BrxB fusion complexed with PglZ f... -

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Basic information

Entry
Database: PDB / ID: 9zn5
TitleHybrid model of a dimer of BrxC-BrxB fusion complexed with PglZ from the Acinetobacter BREX system
Components
  • BrxC-BrxB
  • PglZ
KeywordsANTIMICROBIAL PROTEIN / Restriction / Bacteriophage / Defense / AlphaFold
Biological speciesAcinetobacter sp. NEB 394 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.94 Å
AuthorsDoyle, L.A. / Stoddard, B.L. / Kaiser, B. / Kaiser, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35 GM148166 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R15 GM140375 United States
New England Biolabs United States
CitationJournal: bioRxiv / Year: 2026
Title: Competing forms of protein-protein association and DNA binding exhibited by BrxC from the BREX phage restriction system.
Authors: Alexander J Kaiser / Jennifer J Readshaw / Lindsey A Doyle / Maria Puiu / Abigail Kelly / Sydney F McGuire / Julieta Peralta Acosta / Duc Vu / Andrew Nelson / Darren L Smith / Lidia Araújo- ...Authors: Alexander J Kaiser / Jennifer J Readshaw / Lindsey A Doyle / Maria Puiu / Abigail Kelly / Sydney F McGuire / Julieta Peralta Acosta / Duc Vu / Andrew Nelson / Darren L Smith / Lidia Araújo-Bazán / Ernesto Arias-Palomo / Yvette A Luyten / Barry L Stoddard / Tim R Blower / Brett K Kaiser /
Abstract: Bacteriophage exclusion (BREX) defense systems restrict phage infection via inhibition of phage DNA replication, while also modifying and protecting the bacterial genome. Type I BREX systems encode ...Bacteriophage exclusion (BREX) defense systems restrict phage infection via inhibition of phage DNA replication, while also modifying and protecting the bacterial genome. Type I BREX systems encode six conserved proteins, including a site-specific DNA methyltransferase. Host methylation requires a subset of BREX proteins, whereas phage restriction generally requires them all, suggesting that distinct but overlapping complexes mediate these activities. Full details of the mechanism and regulation of BREX remains to be understood. Here, we characterize the behavior and structures of the conserved BrxC AAA+ ATPase protein. BrxC forms multiple competing assemblages - various self-associating multimers, as well as a complex with BrxB-PglZ - that can be uncoupled via distinct point mutations, leading to differing effects on host methylation versus phage restriction. BrxC's self-association, as well as its ability to bind DNA, is regulated by ATP binding and hydrolysis; BrxA and BrxB appear to also regulate those behaviors. These collective results suggest that BrxC may play a key role in controlling the two activities of BREX, with BrxB, BrxC and PglZ forming a core complex, and the equilibrium among competing assemblies containing those proteins modulating the balance between idling and activated restrictive states.
History
DepositionDec 12, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BrxC-BrxB
B: PglZ
C: BrxC-BrxB
D: PglZ


Theoretical massNumber of molelcules
Total (without water)371,1024
Polymers371,1024
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein BrxC-BrxB


Mass: 85484.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: BrxC truncated to residues 1-553 fused to BrxB with a 2xGGS linker
Source: (gene. exp.) Acinetobacter sp. NEB 394 (bacteria) / Production host: Escherichia coli (E. coli)
#2: Protein PglZ


Mass: 100066.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PglZ with a thrombin scar at the C-terminal / Source: (gene. exp.) Acinetobacter sp. NEB 394 (bacteria) / Production host: Escherichia coli (E. coli)
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: Dimer of BrxC-BrxB fusion complexed with PglZ / Type: COMPLEX
Details: Dimer of fusion of N-terminal BrxC with BrxB complexed to PglZ
Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Acinetobacter sp. NEB 394 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Details: Complex purified in 25 mM Tris pH 7.5 + 150 mM NaCl, with additions of MgCl2, ATP, and CHAPS shortly before grid preparation
Buffer component
IDConc.NameFormulaBuffer-ID
1200 mMSodium chlorideNaCl1
225 mMTris1
31 mMATP1
41 mMMagnesium chlorideMgCl21
50.05 %CHAPS1
SpecimenConc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: 1 mM Magnesium chloride, 1 mM AMP-PMP, and 0.05% CHAPS were added to the sample shortly before grid preparation
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingAverage exposure time: 6 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4012

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.5.3particle selectionBlob Picker
2cryoSPARC4.5.3particle selectionTemplate Picker
5cryoSPARC4.5.3CTF correctionPatch CTF
8ISOLDEmodel fitting
9UCSF ChimeraX1.1model fitting
11cryoSPARC4.5.3initial Euler assignmentAb initio
12cryoSPARC4.5.3initial Euler assignmentHetero Refinement
13cryoSPARC4.5.3final Euler assignmentNon-Uniform Refinement
15cryoSPARC4.5.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 343194
Details: Blob picking on a 500 denoised micrograph resulted in 343,194 particles, which were rigorously sorted/classified and used to generate templates for template picking on the full dataset which ...Details: Blob picking on a 500 denoised micrograph resulted in 343,194 particles, which were rigorously sorted/classified and used to generate templates for template picking on the full dataset which resulted in 2,679,070 particles.
3D reconstructionResolution: 6.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 195504 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Details: Initial model consisted of a fusion of N-terminal BrxC and BrxB complexed with PglZ. The entire model was initially placed into the volume using the ChimeraX Fit in Map tool. Individual ...Details: Initial model consisted of a fusion of N-terminal BrxC and BrxB complexed with PglZ. The entire model was initially placed into the volume using the ChimeraX Fit in Map tool. Individual domains were then manually rotated/translated into the volume and adjusted with Fit in Map. The interface between BrxB and PglZ was preserved by treating the N-terminal domain of PglZ as part of the fusion. The model was then minimally refined with ISOLDE to resolve bond distortions from rigid domain fitting.
Atomic model buildingSource name: AlphaFold / Type: in silico model

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