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- EMDB-50029: Consensus map for the phage immunity methyltransferase protein BrxX -

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Basic information

Entry
Database: EMDB / ID: EMD-50029
TitleConsensus map for the phage immunity methyltransferase protein BrxX
Map data
Sample
  • Complex: BrxX methyltransferase from E. coli
    • Protein or peptide: BrxX methyltransferase from E. coli
KeywordsMethyltransferase / phage defense / BREX / DNA-binding / TRANSFERASE
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.91 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_50029.png

Downloads & links

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Map

FileDownload / File: emd_50029.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: 0.0147
Minimum - Maximum-0.06353815 - 0.17152205
Average (Standard dev.)0.00013430459 (±0.003854692)
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_50029_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_50029_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 : BrxX methyltransferase from E. coli

EntireName: BrxX methyltransferase from E. coli
Components
  • Complex: BrxX methyltransferase from E. coli
    • Protein or peptide: BrxX methyltransferase from E. coli

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Supramolecule #1: BrxX methyltransferase from E. coli

SupramoleculeName: BrxX methyltransferase from E. coli / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: BrxX methyltransferase from E. coli

MacromoleculeName: BrxX methyltransferase from E. coli / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: MNTNNIKKYA PQARNDFRDA VIQKLTTLGI AADKKGNLQI AEAETIGETV RYGQFDYPLS TLPRRERLVK RAREQGFEVL VEHCAYTWFN RLCAIRYMEL HGYLDHGFRM LSHPETPTAF EVLDHVPEVA EALLPESKAQ LVEMKLSGNQ DEALYRELLL GQCHALHHAM ...String:
MNTNNIKKYA PQARNDFRDA VIQKLTTLGI AADKKGNLQI AEAETIGETV RYGQFDYPLS TLPRRERLVK RAREQGFEVL VEHCAYTWFN RLCAIRYMEL HGYLDHGFRM LSHPETPTAF EVLDHVPEVA EALLPESKAQ LVEMKLSGNQ DEALYRELLL GQCHALHHAM PFLFEAVDDE AELLLPDNLT RTDSILRGLV DDIPEEDWEQ VEVIGWLYQF YISEKKDAVI GKVVKSEDIP AATQLFTPNW IVQYLVQNSV GRQWLQTYPD SPLKDKMEYY IEPAEQTPEV QAQLAAITPA SIEPESIKVL DPACGSGHIL TEAYNVLKAI YEERGYRTRD IPQLILENNI FGLDIDDRAA QLSGFAMLML ARQDDRRILG RGVRLNIVSL QESKLDIAEV WTKLNFHQHM QRGSMGDMFT QGTALANTDS AEYKLLMRTL ALFTSAKTLG SLIQVPQEDE AALKAFLERL YRLAVEGDIQ QKEAAAELIP YIQQAWILAQ RYDAVVANPP YMGGKGMNGD LKEFAKKQFP DSKSDLFAMF MQHAFSLLKE NGFNAQVNMQ SWMFLSSYEA LRGWLLDNKT FITMAHLGAR AFGQISGEVV QTTAWVIKNN HSGFYKPVFF RLVDDNEEHK KNNLLNRMNC FKNTLQNDFK KIPGSPIAYW ATLAFINSFL KLPALGTRAV KGLDTNGSID VFLRRWPEVS INSFDALGKG NSKWFPIAKG GELRKWFGNH EYIINYENDG IELRKNKANL RNKDMYFQEG GTWTVVSTTG FSMRYMPKGF LFDQGGSAVF CENNDELSIY NILACMNSKY INYSASLICP TLNFTTGDVR KFPVIKNNHL EDLAKKAIEI SKADWNQFET SWEFSKNKLI EHKGNVAYSY ASYCNFQDKL YEQLVNIEKN INNIIEEILG FKIETTENSE LITLNSNKIY RYGQSETNDT FLNRHRSDTI SELISYSVGC QMGRYSLDRE GLVYAHEGNK GFAELAAEGA YKTFPADNDG ILPLMDDEWF EDDVTSRVKE FVRTVWGEEH LQENLEFIAE SLCLYAIKPK KGESALETIR RYLSTQFWKD HMKMYKKRPI YWLFSSGKEK AFECLVYLHR YNDATLSRMR TEYVVPLLAR YQANIDRLND QLDEASGGEA TRLKRERDSL IKKFSELRSY DDRLRHYADM RISIDLDDGV KVNYGKFGDL LADVKAITGN APEAI

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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: 2.91 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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