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- PDB-9zdx: Dimer of ATPase BrxC containing a Walker B mutation and bound to ... -

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Entry
Database: PDB / ID: 9zdx
TitleDimer of ATPase BrxC containing a Walker B mutation and bound to ATP from the Acinetobacter BREX system
ComponentsBREX system P-loop protein BrxC
KeywordsANTIMICROBIAL PROTEIN / Restriction / Bacteriophage / Defense / AlphaFold
Function / homologyADENOSINE-5'-TRIPHOSPHATE
Function and homology information
Biological speciesAcinetobacter (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.95 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)5R35GM148166 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R15 GM140375 United States
Other privateNew 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
DepositionNov 26, 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
C: BREX system P-loop protein BrxC
A: BREX system P-loop protein BrxC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)280,9156
Polymers279,8522
Non-polymers1,0634
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein BREX system P-loop protein BrxC


Mass: 139925.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter (bacteria) / Gene: SAMN05444586_103019 / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: BrxC Walker B / Type: COMPLEX
Details: BrxC protein from the Acinetobacter BREX system with a Walker B mutation of Glu to Gln in the ATP binding pocket and bound to ATP
Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Acinetobacter (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1200 mMSodium chlorideNaCl1
225 mMTris1
31 mMATP1
42 mMMagnesium chlorideMgCl21
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: 4131

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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
9Coot0.9.8.93model fitting
10Coot1.1.18model fitting
12cryoSPARC4.5.3initial Euler assignmentAb initio
13cryoSPARC4.5.3initial Euler assignmentHetero Refinement
14cryoSPARC4.5.3final Euler assignmentNon-Uniform Refinement
16cryoSPARC4.5.33D reconstruction
17PHENIX1.21.1_5286model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3132271
Details: Blob picking on a 200 micrograph resulted in 112,543 particles, which were rigorously sorted/classified and used to generate templates for template picking on the full dataset
3D reconstructionResolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 477102 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049027
ELECTRON MICROSCOPYf_angle_d0.51812193
ELECTRON MICROSCOPYf_dihedral_angle_d9.211260
ELECTRON MICROSCOPYf_chiral_restr0.0391324
ELECTRON MICROSCOPYf_plane_restr0.0031589

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