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- EMDB-74076: Dimer of ATPase BrxC containing a Walker B mutation and bound to ... -

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Basic information

Entry
Database: EMDB / ID: EMD-74076
TitleDimer of ATPase BrxC containing a Walker B mutation and bound to ATP from the Acinetobacter BREX system
Map dataSharpened map from CryoSPARC Non-Uniform Refinement used in model building
Sample
  • Complex: BrxC Walker B
    • Protein or peptide: BREX system P-loop protein BrxC
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsRestriction / Bacteriophage / Defense / AlphaFold / ANTIMICROBIAL PROTEIN
Biological speciesAcinetobacter (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 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 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
DepositionNov 26, 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_74076.png

Downloads & links

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Map

FileDownload / File: emd_74076.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map from CryoSPARC Non-Uniform Refinement used in model building
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 360 pix.
= 403.92 Å		1.12 Å/pix.
x 360 pix.
= 403.92 Å		1.12 Å/pix.
x 360 pix.
= 403.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.122 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.38
Minimum - Maximum-3.324147 - 5.8372316
Average (Standard dev.)-0.00017092389 (±0.058995724)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 403.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_74076_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Unsharpened map from CryoSPARC Non-Uniform Refinement

Fileemd_74076_additional_1.map
AnnotationUnsharpened map from CryoSPARC Non-Uniform Refinement
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half map A from CryoSPARC Non-Uniform Refinement

Fileemd_74076_half_map_1.map
AnnotationHalf map A from CryoSPARC 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 CryoSPARC Non-Uniform Refinement

Fileemd_74076_half_map_2.map
AnnotationHalf map B from CryoSPARC Non-Uniform Refinement
Projections & Slices
AxesZYX

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Histogram

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Sample components

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Entire : BrxC Walker B

EntireName: BrxC Walker B
Components
  • Complex: BrxC Walker B
    • Protein or peptide: BREX system P-loop protein BrxC
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: BrxC Walker B

SupramoleculeName: BrxC Walker B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: BrxC protein from the Acinetobacter BREX system with a Walker B mutation of Glu to Gln in the ATP binding pocket and bound to ATP
Source (natural)Organism: Acinetobacter (bacteria)

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Macromolecule #1: BREX system P-loop protein BrxC

MacromoleculeName: BREX system P-loop protein BrxC / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter (bacteria)
Molecular weightTheoretical: 139.925797 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SHMNIKELFY KPLDRAINGV VKADQDDNAT VYQELDEYVV TNELEKHFRD FFQSYGTDLS DPSIANRVGV WISGFFGSGK SHFLKTLSY ILANKVARDA EGNERSAAEF FDESKIRDAF IRADIGKAVS HHADVILFNI DSKASSNDDG NPILNVFLRV F NEYQGFSA ...String:
SHMNIKELFY KPLDRAINGV VKADQDDNAT VYQELDEYVV TNELEKHFRD FFQSYGTDLS DPSIANRVGV WISGFFGSGK SHFLKTLSY ILANKVARDA EGNERSAAEF FDESKIRDAF IRADIGKAVS HHADVILFNI DSKASSNDDG NPILNVFLRV F NEYQGFSA DHPHIAHMER HLSQKGVYER FKQAFEESSG MSWLEERDGY QFYQDDVETA ISQALNLSAE AAHKWFEDSE QT FSVSVEN FCQWVKEYLD SKGPQQRMLF LVDQVGQFIG SDTRLMLTLQ TITENLGTIC KGRAWIIVTS QADIDAVLGE MSS SKANDF SKIAGRFKTR LSLSSSNTDE VIQKRLLRKT PEAEALLRSV FEQKGDILKN QITFDRSGPT LKNYEGPDSF IHNY PFAPY HFQLVQKVFE EIRKVGATGA HLAYGERSML DAFQMAANAI ATDEVGALVP FHRFYTSVEG FLDTAVKRTI DQAGQ NKTL DGFDVQMLRT LFMIRYVDII KGTLDNLVTL SIEKIDEDKL ALRKRIEESL QRLEKESLIT RNGDEFLFLT NEERDI TRK IKATDLAASE ENKELANLIF KDLLRDQNKY RHQANKMDYQ IGRFLDSHSL DGKYESDLKV EIISPLDTEY NLYTEAY CI GKSTQAEGQV LFKLADDKQF FNELRTWLKT NKFIRLNDDG TQSDISRILA DRGRENQERK KRLRARVEEM LLDAESYA L GQHLQLSSSS PTTKLDEACR YLLENTYTKL SYLQVYQQDA WRELNAVLTV DDMAQLGLSL DGGQSNPKAL QEVEQYIAL RATGSERILV SDVIDRFVKR PYGWPDAEIL LLVGQLAAMG RISLQLNGGS LQLKDAFEPL QNSRRRRDVS IIKKRQTDDQ VLKQARQLT QDLFSAMGPA TEKELFEFYT QHFKNWLANF KSYKSKTDVG QFPGKKVIEK SILTLERLLA NSDSFDFFKA V VENKDDYL DLEEDYRDIH EFFTNQMPSW QQLQQALRHF EKNKQALGSD EVAKKALSEL HRIATLESPY GLLNKVADLV RT VESVNEQ LLTEKRNQAI EHIDDKIKQL EAEIKNSGIA SAELSNKLLR PLQLLKTDIE VESSLSTIYM LQTQTSVERF DEA LYELER EVQAEIQRQA KAAQLAQSKA ESVTNTATTS SPATSAPAAS PVQPVTAVVP PKPVVEVDVA SIYSKSSSSV YLET EESVD QFVDALKAEL KKIVGDKKRV RIR

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
200.0 mMNaClSodium chloride
25.0 mMTris
1.0 mMATP
2.0 mMMgCl2Magnesium chloride
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

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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: 4131 / 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: 3132271
Details: Blob picking on a 200 micrograph resulted in 112,543 particles, which were rigorously sorted/classified and used to generate templates for template picking on the full dataset
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 dimer of BrxC
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 477102
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Software:
Namedetails
cryoSPARC (ver. 4.5.3)Ab initio
cryoSPARC (ver. 4.5.3)Hetero Refinement

Details: Initial reconstruction done on particles picked from a 200 micrograph subset and classified, followed by hetero refinement. The best classes were used for template picking of particles from ...Details: Initial reconstruction done on particles picked from a 200 micrograph subset and classified, followed by hetero refinement. The best classes were used for template picking of particles from the full dataset and those picks were applied to a hetero refinement job using the volumes from to initial hetero refinement of the subset.
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
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9zdx:
Dimer of ATPase BrxC containing a Walker B mutation and bound to ATP from the Acinetobacter BREX system

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