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- EMDB-74400: Volume of PglZ in complex with BrxB-BrxC fusion from the Acinetob... -

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Basic information

Entry
Database: EMDB / ID: EMD-74400
TitleVolume of PglZ in complex with BrxB-BrxC fusion from the Acinetobacter BREX system
Map dataSharpened map from Non-Uniform Refinement
Sample
  • Complex: PglZ in complex with truncated BrxC-BrxB fusion
    • Protein or peptide: PglZ
    • Protein or peptide: BrxC-BrxB
KeywordsRestriction / Bacteriophage / Defense / AlphaFold / ANTIMICROBIAL PROTEIN
Biological speciesAcinetobacter (bacteria) / Acinetobacter sp. NEB 394 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.46 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)5R35GM148166 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R15 GM140375 United States
Other privateNew England Biolabs
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 8, 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_74400.png

Downloads & links

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Map

FileDownload / File: emd_74400.map.gz / Format: CCP4 / Size: 103 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.)
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: 0.275
Minimum - Maximum-2.7399266 - 4.000068
Average (Standard dev.)0.0005457585 (±0.07073635)
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_74400_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_74400_msk_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: Unsharpened map from Non-Uniform Refinement

Fileemd_74400_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 B from Non-Uniform Refinement

Fileemd_74400_half_map_1.map
AnnotationHalf map B 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 A from Non-Uniform Refinement

Fileemd_74400_half_map_2.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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Sample components

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Entire : PglZ in complex with truncated BrxC-BrxB fusion

EntireName: PglZ in complex with truncated BrxC-BrxB fusion
Components
  • Complex: PglZ in complex with truncated BrxC-BrxB fusion
    • Protein or peptide: PglZ
    • Protein or peptide: BrxC-BrxB

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Supramolecule #1: PglZ in complex with truncated BrxC-BrxB fusion

SupramoleculeName: PglZ in complex with truncated BrxC-BrxB fusion / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: PglZ in complex with a fusion of truncated BrxC and BrxB from the Acinetobacter BREX system
Source (natural)Organism: Acinetobacter (bacteria)
Molecular weightTheoretical: 185 KDa

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Macromolecule #1: PglZ

MacromoleculeName: PglZ / type: protein_or_peptide / ID: 1 / Details: PglZ with a thrombin scar at the C-termini / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter sp. NEB 394 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGNLSQLQQG LEQAFFHENH RIVFWYDAEQ SFTEEIKALE LNDVHILNMA EESSLAIKLK LELEDQQGKY LLYFPSPEPE TEKDWLLDIK LYSRSFYADR FSIIFNELGL QQQSLREHLA KREEFLKAKA RLSTLKRYIQ PDADAQDLDM AMIAAVVKAD SAELMHIVLA ...String:
MGNLSQLQQG LEQAFFHENH RIVFWYDAEQ SFTEEIKALE LNDVHILNMA EESSLAIKLK LELEDQQGKY LLYFPSPEPE TEKDWLLDIK LYSRSFYADR FSIIFNELGL QQQSLREHLA KREEFLKAKA RLSTLKRYIQ PDADAQDLDM AMIAAVVKAD SAELMHIVLA LADEMVQQNL GLEVNPDSFA ELEKFQLVPA LVTALQAEIG YPASVEELNG EAPFKLGTFF IRLMTTGFCE SLGDIPLWAQ ELVMSSVSSR ATARAFLSRW RDSSKYYPTF DTLSQTVANA LRIQEKVGAF DLEQLLDVMT FEVIEQKIIV DLASQIPAAA KAELEHFRTV ISTRLDGYWA SKHKDDATRR KYRTVYTALQ AAIELFSLRL QFDSGFYFDS SEALYKAYEQ ELYRFDMAYR HYSAASQRAH VDILKKLDEE VENCYSYWFI DHLARNWGER VEAEQRLNVW KVADIPNQQN FYDTHVRSLL GSATKRRIVV IISDAFRYEA AVELRDRINE KRYSEATLSS QLGVVPSYTT LGMASLLPHQ TLEYKEAAGD DVLVDGQSSK GTAARSKILA AYNGLAVTAE MVKGWSRDEG REALKDHELI YVYHNVIDAR GDSASTESET FMAVEHAIEE LTELSRKILM HFNISTLLIT ADHGFLFQQS KLESADRSSL TEKPTNTLKS KKRYVIGHGL PESKEAWKGS TQATAGTLSA TDFWIPKGAN RFHFVGGSRF VHGGIMPQEI VVPVLMVKQL RGEKAGQRTK RKVEVISTKS TLKMVNNIQK FDLMQTEAVS ELVMPVTLSI AIYDGDLKVS SEETLTFDSS TDSVADRVKQ VRLSLSGTDF DRKKDYFLVL KDKDLNIEMQ RYKVTIDLAF TDDFFLVPR

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Macromolecule #2: BrxC-BrxB

MacromoleculeName: BrxC-BrxB / type: protein_or_peptide / ID: 2
Details: Thrombin cleavage scar (GS), pET vector artifact (HMG), BrxC truncated to residues 1-553, linker (GGSGGS), BrxB
Enantiomer: LEVO
Source (natural)Organism: Acinetobacter sp. NEB 394 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSHMGNIKEL FYKPLDRAIN GVVKADQDDN ATVYQELDEY VVTNELEKHF RDFFQSYGTD LSDPSIANRV GVWISGFFGS GKSHFLKTLS YILANKVARD AEGNERSAAE FFDESKIRDA FIRADIGKAV SHHADVILFN IDSKASSNDD GNPILNVFLR VFNEYQGFSA ...String:
GSHMGNIKEL FYKPLDRAIN GVVKADQDDN ATVYQELDEY VVTNELEKHF RDFFQSYGTD LSDPSIANRV GVWISGFFGS GKSHFLKTLS YILANKVARD AEGNERSAAE FFDESKIRDA FIRADIGKAV SHHADVILFN IDSKASSNDD GNPILNVFLR VFNEYQGFSA DHPHIAHMER HLSQKGVYER FKQAFEESSG MSWLEERDGY QFYQDDVETA ISQALNLSAE AAHKWFEDSE QTFSVSVENF CQWVKEYLDS KGPQQRMLFL VDEVGQFIGS DTRLMLTLQT ITENLGTICK GRAWIIVTSQ ADIDAVLGEM SSSKANDFSK IAGRFKTRLS LSSSNTDEVI QKRLLRKTPE AEALLRSVFE QKGDILKNQI TFDRSGPTLK NYEGPDSFIH NYPFAPYHFQ LVQKVFEEIR KVGATGAHLA YGERSMLDAF QMAANAIATD EVGALVPFHR FYTSVEGFLD TAVKRTIDQA GQNKTLDGFD VQMLRTLFMI RYVDIIKGTL DNLVTLSIEK IDEDKLALRK RIEESLQRLE KESLITRNGD EFLFLTNGGS GGSMSQTIHE RLNQIPERIL STEFLTGQGL GNEIGFWIFD YAPEDELKVR EYLHFLDGML EKKHSQLKVV NINLLQAVVD YLAERNFIDK AIQMQKAKGD EALLKALKGP LHMDKFAPYL VSKYATNAQD IVLMTGVGSV WPLLRAHHLL NSLHSLLGHK PVVLFYPGYY DGQAMSLFGK IPSNNYYRAF RLVP

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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

Concentration0.44 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloride
25.0 mMTris
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
DetailsDiluted to final concentration with freshly prepared 25 mM Tris pH 7.5 + 150 mM NaCl

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Electron microscopy

MicroscopeTFS GLACIOS
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 8184 pixel / Digitization - Dimensions - Height: 11520 pixel / Number grids imaged: 1 / Number real images: 3965 / 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
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 4784163
Details: Blob picking on 3602 curated exposures using an elliptical blob with min and max particle diameter of 60 and 170 angstroms.
CTF correctionSoftware - Name: cryoSPARC (ver. 4.2.1) / Software - details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold
Details: AlphaFold model of PglZ complexed with truncated BrxC fused to BrxB
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 101355
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Software:
Namedetails
cryoSPARC (ver. 4.2.1)Ab initio
cryoSPARC (ver. 4.2.1)2D Classification

Details: Particles were split into two sets of equal number (leaving 1 remaining unassigned particle), 2D classified and run through Ab initio reconstruction with 3 classes
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1) / 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: UCSF ChimeraX / Details: Fit in Map
DetailsFitting was primarily done with the ChimeraX Fit in Map tool. PglZ domains were individually fit to the volume, with the PglZ-BrxB interface preserved by treating the N-terminal PglZ domain (residues 1-98) as part of the BrxC-BrxB fusion.
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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