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- EMDB-50028: Focused map for NTD and MTD domains of the phage immunity methylt... -

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Basic information

Entry
Database: EMDB / ID: EMD-50028
TitleFocused map for NTD and MTD domains of the phage immunity methyltransferase protein BrxX.
Map data
Sample
  • Complex: N-terminal domain (NTD) and methyltransferase domain (MTD) from BrxX
    • Protein or peptide: The NTD and MTD from the methyltransferase protein BrxX of the BREX bacterial defense system
KeywordsMethyltransferase / phage defense / BREX / DNA-binding / TRANSFERASE
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsAdams MC / Ghilarov D
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust221868/Z/20/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X01/097X/1 United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: Molecular basis of foreign DNA recognition by BREX anti-phage immunity system.
Authors: Alena Drobiazko / Myfanwy C Adams / Mikhail Skutel / Kristina Potekhina / Oksana Kotovskaya / Anna Trofimova / Mikhail Matlashov / Daria Yatselenko / Karen L Maxwell / Tim R Blower / ...Authors: Alena Drobiazko / Myfanwy C Adams / Mikhail Skutel / Kristina Potekhina / Oksana Kotovskaya / Anna Trofimova / Mikhail Matlashov / Daria Yatselenko / Karen L Maxwell / Tim R Blower / Konstantin Severinov / Dmitry Ghilarov / Artem Isaev /
Abstract: Anti-phage systems of the BREX (BacteRiophage EXclusion) superfamily rely on site-specific epigenetic DNA methylation to discriminate between the host and invading DNA. We demonstrate that in Type I ...Anti-phage systems of the BREX (BacteRiophage EXclusion) superfamily rely on site-specific epigenetic DNA methylation to discriminate between the host and invading DNA. We demonstrate that in Type I BREX systems, defense and methylation require BREX site DNA binding by the BrxX (PglX) methyltransferase employing S-adenosyl methionine as a cofactor. We determined 2.2-Å cryoEM structure of Escherichia coli BrxX bound to target dsDNA revealing molecular details of BREX DNA recognition. Structure-guided engineering of BrxX expands its DNA specificity and dramatically enhances phage defense. We show that BrxX alone does not methylate DNA, and BREX activity requires an assembly of a supramolecular BrxBCXZ immune complex. Finally, we present a cryoEM structure of BrxX bound to a phage-encoded inhibitor Ocr that sequesters BrxX in an inactive dimeric form. We propose that BrxX-mediated foreign DNA sensing is a necessary first step in activation of BREX defense.
History
DepositionApr 5, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50028.png

Downloads & links

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Map

FileDownload / File: emd_50028.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 480 pix.
= 326.4 Å		0.68 Å/pix.
x 480 pix.
= 326.4 Å		0.68 Å/pix.
x 480 pix.
= 326.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0372
Minimum - Maximum-0.06427572 - 0.15919428
Average (Standard dev.)0.00012787932 (±0.0033547916)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 326.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_50028_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_50028_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : N-terminal domain (NTD) and methyltransferase domain (MTD) from BrxX

EntireName: N-terminal domain (NTD) and methyltransferase domain (MTD) from BrxX
Components
  • Complex: N-terminal domain (NTD) and methyltransferase domain (MTD) from BrxX
    • Protein or peptide: The NTD and MTD from the methyltransferase protein BrxX of the BREX bacterial defense system

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Supramolecule #1: N-terminal domain (NTD) and methyltransferase domain (MTD) from BrxX

SupramoleculeName: N-terminal domain (NTD) and methyltransferase domain (MTD) from BrxX
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: The NTD and MTD from the methyltransferase protein BrxX of the BR...

MacromoleculeName: The NTD and MTD from the methyltransferase protein BrxX of the BREX bacterial defense system
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
SequenceString: MNTNNIKKYA PQARNDFRDA VIQKLTTLGI AADKKGNLQI AEAETIGETV RYGQFDYPLS TLPRRERLVK RAREQGFEVL VEHCAYTWF NRLCAIRYME LHGYLDHGFR MLSHPETPTA FEVLDHVPEV AEALLPESKA QLVEMKLSGN QDEALYRELL L GQCHALHH ...String:
MNTNNIKKYA PQARNDFRDA VIQKLTTLGI AADKKGNLQI AEAETIGETV RYGQFDYPLS TLPRRERLVK RAREQGFEVL VEHCAYTWF NRLCAIRYME LHGYLDHGFR MLSHPETPTA FEVLDHVPEV AEALLPESKA QLVEMKLSGN QDEALYRELL L GQCHALHH AMPFLFEAVD DEAELLLPDN LTRTDSILRG LVDDIPEEDW EQVEVIGWLY QFYISEKKDA VIGKVVKSED IP AATQLFT PNWIVQYLVQ NSVGRQWLQT YPDSPLKDKM EYYIEPAEQT PEVQAQLAAI TPASIEPESI KVLDPACGSG HIL TEAYNV LKAIYEERGY RTRDIPQLIL ENNIFGLDID DRAAQLSGFA MLMLARQDDR RILGRGVRLN IVSLQESKLD IAEV WTKLN FHQHMQRGSM GDMFTQGTAL ANTDSAEYKL LMRTLALFTS AKTLGSLIQV PQEDEAALKA FLERLYRLAV EGDIQ QKEA AAELIPYIQQ AWILAQRYDA VVANPPYMGG KGMNGDLKEF AKKQFPDSKS DLFAMFMQHA FSLLKENGFN AQVNMQ SWM FLSSYEALRG WLLDNKTFIT MAHLGARAFG QISGEVVQTT AWVIKNNHSG FYKPVFFRLV DDNEEHKKNN LLNRMNC

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 35.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 94764
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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