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- EMDB-74435: Dimer of BrxC-BrxB fusion complexed with PglZ from the Acinetobac... -

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Basic information

Entry
Database: EMDB / ID: EMD-74435
TitleDimer of BrxC-BrxB fusion complexed with PglZ from the Acinetobacter BREX system
Map dataSharpened map from Non-Uniform Refinement
Sample
  • Complex: Dimer of BrxC-BrxB fusion complexed with PglZ
    • Protein or peptide: BrxC-BrxB
    • Protein or peptide: PglZ
KeywordsRestriction / Bacteriophage / Defense / AlphaFold / ANTIMICROBIAL PROTEIN
Biological speciesAcinetobacter sp. NEB 394 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.94 Å
AuthorsDoyle LA / Stoddard BL / Kaiser B / Kaiser A
Funding support United States, 3 items
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 LA
History
DepositionDec 12, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74435.png

Downloads & links

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Map

FileDownload / File: emd_74435.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map from Non-Uniform Refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.24 Å/pix.
x 200 pix.
= 448.8 Å		2.24 Å/pix.
x 200 pix.
= 448.8 Å		2.24 Å/pix.
x 200 pix.
= 448.8 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.244 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.0915338 - 2.182861
Average (Standard dev.)0.0001333928 (±0.045261804)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 448.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_74435_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_74435_msk_2.map
Projections & Slices
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Additional map: Unsharpened map from Non-Uniform Refinement

Fileemd_74435_additional_1.map
AnnotationUnsharpened map from Non-Uniform Refinement
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A from Non-Uniform Refinement

Fileemd_74435_half_map_1.map
AnnotationHalf map A from Non-Uniform Refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B from Non-Uniform Refinement

Fileemd_74435_half_map_2.map
AnnotationHalf map B from Non-Uniform Refinement
Projections & Slices
AxesZYX

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Histogram

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Sample components

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Entire : Dimer of BrxC-BrxB fusion complexed with PglZ

EntireName: Dimer of BrxC-BrxB fusion complexed with PglZ
Components
  • Complex: Dimer of BrxC-BrxB fusion complexed with PglZ
    • Protein or peptide: BrxC-BrxB
    • Protein or peptide: PglZ

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Supramolecule #1: Dimer of BrxC-BrxB fusion complexed with PglZ

SupramoleculeName: Dimer of BrxC-BrxB fusion complexed with PglZ / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Dimer of fusion of N-terminal BrxC with BrxB complexed to PglZ
Source (natural)Organism: Acinetobacter sp. NEB 394 (bacteria)

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Macromolecule #1: BrxC-BrxB

MacromoleculeName: BrxC-BrxB / type: protein_or_peptide / ID: 1
Details: BrxC truncated to residues 1-553 fused to BrxB with a 2xGGS linker
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter sp. NEB 394 (bacteria)
Molecular weightTheoretical: 85.484484 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSHMGNIKEL FYKPLDRAIN GVVKADQDDN ATVYQELDEY VVTNELEKHF RDFFQSYGTD LSDPSIANRV GVWISGFFGS GKSHFLKTL SYILANKVAR DAEGNERSAA EFFDESKIRD AFIRADIGKA VSHHADVILF NIDSKASSND DGNPILNVFL R VFNEYQGF ...String:
GSHMGNIKEL FYKPLDRAIN GVVKADQDDN ATVYQELDEY VVTNELEKHF RDFFQSYGTD LSDPSIANRV GVWISGFFGS GKSHFLKTL SYILANKVAR DAEGNERSAA EFFDESKIRD AFIRADIGKA VSHHADVILF NIDSKASSND DGNPILNVFL R VFNEYQGF SADHPHIAHM ERHLSQKGVY ERFKQAFEES SGMSWLEERD GYQFYQDDVE TAISQALNLS AEAAHKWFED SE QTFSVSV ENFCQWVKEY LDSKGPQQRM LFLVDEVGQF IGSDTRLMLT LQTITENLGT ICKGRAWIIV TSQADIDAVL GEM SSSKAN DFSKIAGRFK TRLSLSSSNT DEVIQKRLLR KTPEAEALLR SVFEQKGDIL KNQITFDRSG PTLKNYEGPD SFIH NYPFA PYHFQLVQKV FEEIRKVGAT GAHLAYGERS MLDAFQMAAN AIATDEVGAL VPFHRFYTSV EGFLDTAVKR TIDQA GQNK TLDGFDVQML RTLFMIRYVD IIKGTLDNLV TLSIEKIDED KLALRKRIEE SLQRLEKESL ITRNGDEFLF LTNGGS GGS MSQTIHERLN QIPERILSTE FLTGQGLGNE IGFWIFDYAP EDELKVREYL HFLDGMLEKK HSQLKVVNIN LLQAVVD YL AERNFIDKAI QMQKAKGDEA LLKALKGPLH MDKFAPYLVS KYATNAQDIV LMTGVGSVWP LLRAHHLLNS LHSLLGHK P VVLFYPGYYD GQAMSLFGKI PSNNYYRAFR LVP

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Macromolecule #2: PglZ

MacromoleculeName: PglZ / type: protein_or_peptide / ID: 2 / Details: PglZ with a thrombin scar at the C-terminal / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter sp. NEB 394 (bacteria)
Molecular weightTheoretical: 100.066445 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGNLSQLQQG LEQAFFHENH RIVFWYDAEQ SFTEEIKALE LNDVHILNMA EESSLAIKLK LELEDQQGKY LLYFPSPEPE TEKDWLLDI KLYSRSFYAD RFSIIFNELG LQQQSLREHL AKREEFLKAK ARLSTLKRYI QPDADAQDLD MAMIAAVVKA D SAELMHIV ...String:
MGNLSQLQQG LEQAFFHENH RIVFWYDAEQ SFTEEIKALE LNDVHILNMA EESSLAIKLK LELEDQQGKY LLYFPSPEPE TEKDWLLDI KLYSRSFYAD RFSIIFNELG LQQQSLREHL AKREEFLKAK ARLSTLKRYI QPDADAQDLD MAMIAAVVKA D SAELMHIV LALADEMVQQ NLGLEVNPDS FAELEKFQLV PALVTALQAE IGYPASVEEL NGEAPFKLGT FFIRLMTTGF CE SLGDIPL WAQELVMSSV SSRATARAFL SRWRDSSKYY PTFDTLSQTV ANALRIQEKV GAFDLEQLLD VMTFEVIEQK IIV DLASQI PAAAKAELEH FRTVISTRLD GYWASKHKDD ATRRKYRTVY TALQAAIELF SLRLQFDSGF YFDSSEALYK AYEQ ELYRF DMAYRHYSAA SQRAHVDILK KLDEEVENCY SYWFIDHLAR NWGERVEAEQ RLNVWKVADI PNQQNFYDTH VRSLL GSAT KRRIVVIISD AFRYEAAVEL RDRINEKRYS EATLSSQLGV VPSYTTLGMA SLLPHQTLEY KEAAGDDVLV DGQSSK GTA ARSKILAAYN GLAVTAEMVK GWSRDEGREA LKDHELIYVY HNVIDARGDS ASTESETFMA VEHAIEELTE LSRKILM HF NISTLLITAD HGFLFQQSKL ESADRSSLTE KPTNTLKSKK RYVIGHGLPE SKEAWKGSTQ ATAGTLSATD FWIPKGAN R FHFVGGSRFV HGGIMPQEIV VPVLMVKQLR GEKAGQRTKR KVEVISTKST LKMVNNIQKF DLMQTEAVSE LVMPVTLSI AIYDGDLKVS SEETLTFDSS TDSVADRVKQ VRLSLSGTDF DRKKDYFLVL KDKDLNIEMQ RYKVTIDLAF TDDFFLVPR

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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

Concentration3.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
200.0 mMNaClSodium chloride
25.0 mMTris
1.0 mMATP
1.0 mMMgCl2Magnesium chloride
0.05 %CHAPS

Details: Complex purified in 25 mM Tris pH 7.5 + 150 mM NaCl, with additions of MgCl2, ATP, and CHAPS shortly before grid preparation
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 20 / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details1 mM Magnesium chloride, 1 mM AMP-PMP, and 0.05% CHAPS were added to the sample shortly before grid preparation

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 4012 / Average exposure time: 6.0 sec. / Average electron dose: 50.0 e/Å2
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

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Image processing

Particle selectionNumber 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.
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Software - details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold / Details: AlphaFold of BrxC-BrxB fusion complexed with PglZ
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 195504
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Software:
Namedetails
cryoSPARC (ver. 4.5.3)Ab initio
cryoSPARC (ver. 4.5.3)Hetero Refinement
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3) / Software - details: Non-Uniform Refinement
Final 3D classificationNumber classes: 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
SoftwareName: ISOLDE
DetailsInitial 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.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9zn5:
Hybrid model of a dimer of BrxC-BrxB fusion complexed with PglZ from the Acinetobacter BREX system

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