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- EMDB-49827: Complex of BREX proteins BrxB and PglZ from Salmonella typhimurium -

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Basic information

Entry
Database: EMDB / ID: EMD-49827
TitleComplex of BREX proteins BrxB and PglZ from Salmonella typhimurium
Map dataSharpened map
Sample
  • Complex: Complex of BREX proteins BrxB / PglZ from Salmonella Typhimurium str. D23580
    • Protein or peptide: DUF1788 domain-containing protein
    • Protein or peptide: PglZ domain-containing protein
KeywordsRestriction / Bacteriophage / Defense / BREX / Salmonella typhimurium / Salmonella / AlphaFold / ANTIMICROBIAL PROTEIN
Function / homologyAlkaline phosphatase-like protein PglZ / BREX protein BrxB / BREX protein BrxB / PglZ domain / PglZ domain / Alkaline-phosphatase-like, core domain superfamily / PglZ domain-containing protein / DUF1788 domain-containing protein
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. D23580 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.45 Å
AuthorsDoyle LA / Stoddard B / Blower TR / Kaiser B
Funding support United Kingdom, United States, 7 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/Y003659/1 United Kingdom
The Lister Institute of Preventive Medicine United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T008695/1 United Kingdom
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)GM140375 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)5 P30 CA015704-49 United States
Other private
CitationJournal: Nucleic Acids Res / Year: 2025
Title: PglZ from Type I BREX phage defence systems is a metal-dependent nuclease that forms a sub-complex with BrxB.
Authors: Jennifer J Readshaw / Lindsey A Doyle / Maria Puiu / Abigail Kelly / Andrew Nelson / Alex J Kaiser / Sydney F McGuire / Julieta Peralta Acosta / Darren L Smith / Barry L Stoddard / Brett K ...Authors: Jennifer J Readshaw / Lindsey A Doyle / Maria Puiu / Abigail Kelly / Andrew Nelson / Alex J Kaiser / Sydney F McGuire / Julieta Peralta Acosta / Darren L Smith / Barry L Stoddard / Brett K Kaiser / Tim R Blower /
Abstract: BREX (Bacteriophage Exclusion) systems, identified through shared identity with Pgl (Phage Growth Limitation) systems, are a widespread, highly diverse group of phage defence systems found throughout ...BREX (Bacteriophage Exclusion) systems, identified through shared identity with Pgl (Phage Growth Limitation) systems, are a widespread, highly diverse group of phage defence systems found throughout bacteria and archaea. The varied BREX Types harbour multiple protein subunits (between four and eight) and all encode a conserved putative phosphatase, PglZ, and an equally conserved, putative ATPase, BrxC. Almost all BREX systems also contain a site-specific methyltransferase, PglX. Despite having determined the structure and fundamental biophysical and biochemical behaviours of several BREX factors (including the PglX methyltransferase, the BrxL effector, the BrxA DNA-binding protein, and a commonly-associated transcriptional regulator, BrxR), the mechanism by which BREX impedes phage replication remains largely undetermined. In this study, we identified a stable BREX sub-complex of PglZ:BrxB, generated and validated a structural model of that protein complex, and assessed the biochemical activity of PglZ from BREX, revealing it to be a metal-dependent nuclease. PglZ can cleave cyclic oligonucleotides, linear oligonucleotides, plasmid DNA and both non-modified and modified linear phage genomes. PglZ nuclease activity has no obvious role in BREX-dependent methylation, but does contribute to BREX phage defence. BrxB binding does not impact PglZ nuclease activity. These data contribute to our growing understanding of BREX phage defence.
History
DepositionMar 20, 2025-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49827.png

Downloads & links

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Map

FileDownload / File: emd_49827.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 300 pix.
= 336.6 Å		1.12 Å/pix.
x 300 pix.
= 336.6 Å		1.12 Å/pix.
x 300 pix.
= 336.6 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.122 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.27
Minimum - Maximum-1.9594486 - 3.3819268
Average (Standard dev.)0.0011284727 (±0.05579652)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 336.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49827_msk_1.map
Projections & Slices
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Additional map: Unsharpened map from non-uniform refinement

Fileemd_49827_additional_1.map
AnnotationUnsharpened map from non-uniform refinement
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Half map: Half map A

Fileemd_49827_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

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Half map: Half map B

Fileemd_49827_half_map_2.map
AnnotationHalf map B
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Sample components

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Entire : Complex of BREX proteins BrxB / PglZ from Salmonella Typhimurium ...

EntireName: Complex of BREX proteins BrxB / PglZ from Salmonella Typhimurium str. D23580
Components
  • Complex: Complex of BREX proteins BrxB / PglZ from Salmonella Typhimurium str. D23580
    • Protein or peptide: DUF1788 domain-containing protein
    • Protein or peptide: PglZ domain-containing protein

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Supramolecule #1: Complex of BREX proteins BrxB / PglZ from Salmonella Typhimurium ...

SupramoleculeName: Complex of BREX proteins BrxB / PglZ from Salmonella Typhimurium str. D23580
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. D23580 (bacteria)

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Macromolecule #1: DUF1788 domain-containing protein

MacromoleculeName: DUF1788 domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. D23580 (bacteria)
Molecular weightTheoretical: 22.867256 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: IDPVLEYRLS QVQSRISEER FLKNNGSGNE IGFWIFDYPA QNELQVREHL KYLLRNLEKD HKFAHLNIFQ IIVDMLTERG LFDRVCQQE VKVGTEALKK QLVGLLNQKK IADYIAKKVD LQNQEFVILT GMGNAWPLVR GHELMSALQD VMGFTPLLMF Y PGTYSGHD ...String:
IDPVLEYRLS QVQSRISEER FLKNNGSGNE IGFWIFDYPA QNELQVREHL KYLLRNLEKD HKFAHLNIFQ IIVDMLTERG LFDRVCQQE VKVGTEALKK QLVGLLNQKK IADYIAKKVD LQNQEFVILT GMGNAWPLVR GHELMSALQD VMGFTPLLMF Y PGTYSGHD LSPLAGIDSR NYYRAFRLVP ESGPAATLNP R

UniProtKB: DUF1788 domain-containing protein

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Macromolecule #2: PglZ domain-containing protein

MacromoleculeName: PglZ domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. D23580 (bacteria)
Molecular weightTheoretical: 102.665305 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTLQNQEFIA GLKAKFAEHR IVFWHDPDKR FLEELDNLEL ENVTLLDMTD QSQLAVKKRI EIDEPEQQFL LWFPHDAPPK EFDWLLDIR LYSTEFHADF AAITLNTLGI PQLGLREHIQ RRKAFFSTKR LSALKGLVTE QENEASLDKK MVAVIAGVKT A KTEEILFS ...String:
MTLQNQEFIA GLKAKFAEHR IVFWHDPDKR FLEELDNLEL ENVTLLDMTD QSQLAVKKRI EIDEPEQQFL LWFPHDAPPK EFDWLLDIR LYSTEFHADF AAITLNTLGI PQLGLREHIQ RRKAFFSTKR LSALKGLVTE QENEASLDKK MVAVIAGVKT A KTEEILFS LITQYVNQQK DDDSDLENTL AMLKRHDLEG VLWDILNQEM GYQAEHPTLE NLILKLFCTD LSAQADPQKR EW LEKNVLA TPSGRASALA FMVTWRADRR YKEAYDYCAQ QMQDALRPED QYRLSSPYDL HECETTLSIE QTIIHALVTQ LLE ESTTLD REAFKKLLSE RQSKYWCQTR QEYCAIYDAL RQAERLLNLR NRHIDGFHYQ DSATFWKAYC EELFRFDQAY RLFN EYALL VHSKGAMILK SLDDYIEALY SNWYLAELSR SWNKVLETEN RMQEWRIAGV PRQQNFYNEV VKPQFNNPQI KRVFV IISD ALRYEVAEEL GNQINTEKRF TAELRSQLGV LPSYTQLGMA ALLPHDEICY QPGSGDIVYA DGLSTSGTPN RDTILK KYK GMAVKSDDLL KWKNQQGRDL IRDYEVVYIW HNTIDAMGDS ASTEEKTFEA CRNAVVELKD LVTRVINRLH GTRIIVT AD HGFLFQQQPL SGQDKTTLQI KPDNTIKNHK RFIIGHQLPA DDFCWKGKVA DTAGVSDNSE FLIPKGIQRF HFSGGARF V HGGAMLQEVC VPVLQVKALQ KTAAEKQPQR RPVDIVKHHP LIKLVNNIDK VSLLQTHPVG ELYEPRTLNI FIVDNANNV VSGKERICFD SDNNTMEKRV RDVTLKLIGA NFNRRNEYWL ILEDAQTETG YQKYPVIIDL AFQDDFFKET AAAKFERQHM DSSTSAA

UniProtKB: PglZ domain-containing protein

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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
Component:
ConcentrationFormulaName
300.0 mMKClPotassium chloride
20.0 mMTris
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 9417 / Average exposure time: 6.0 sec. / Average electron dose: 50.0 e/Å2 / Details: 4686 from grid 1 and 4731 from grid 2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 36000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 15593169
Details: 10,876,932 from blob picking on dataset 1 4,716,237 from template picking on dataset 2
CTF correctionSoftware - Name: cryoSPARC (ver. 4.2.1) / Software - details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 123964
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsAlphaFold model, split into domains at "hinge" points, was rigid fit into the cryo-EM map. The following domains were used: (1) BrxB + 1-96 PglZ, (2) 97-292 PglZ, (3) 293-748 PglZ, and (4) 749-867 PglZ. The model was then simulated in the ISOLDE plug-in for ChimeraX to resolve distortions from rigid domain fitiing.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9nv3:
Hybrid model of a complex of BREX proteins BrxB and PglZ from Salmonella typhimurium

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