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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: To Be Published
Title: Competing forms of protein-protein association and DNA binding exhibited by BrxC from the BREX phage restriction system
Authors: Doyle, L.A.
History
DepositionDec 12, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Mask / Part number: 2 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: 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
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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