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- PDB-8emh: CryoEM characterization of a unique AAA+ BrxL phage restriction factor -

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Basic information

Entry
Database: PDB / ID: 8emh
TitleCryoEM characterization of a unique AAA+ BrxL phage restriction factor
Components
  • DNA (63-MER)
  • DNA (64-MER)
  • Protease Lon-related BREX system protein BrxL
KeywordsANTIMICROBIAL PROTEIN / phage restriction factor / AAA+ protein
Function / homology
Function and homology information


ATP-dependent peptidase activity / protein catabolic process / serine-type endopeptidase activity / proteolysis / ATP binding
Similarity search - Function
Lon-like protease BrxL / Lon-like protease BrxL-like / BREX system Lon protease-like BrxL, N-terminal / Lon-like protease BrxL-like, ATPase domain / BREX system Lon protease-like protein BrxL N-terminal / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 ...Lon-like protease BrxL / Lon-like protease BrxL-like / BREX system Lon protease-like BrxL, N-terminal / Lon-like protease BrxL-like, ATPase domain / BREX system Lon protease-like protein BrxL N-terminal / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Protease Lon-related BREX system protein BrxL
Similarity search - Component
Biological speciesAcinetobacter sp. NEB 394 (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsShen, B.W. / Stoddard, B.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1 GM105691 United States
CitationJournal: Nucleic Acids Res / Year: 2023
Title: Structure, substrate binding and activity of a unique AAA+ protein: the BrxL phage restriction factor.
Authors: Betty W Shen / Lindsey A Doyle / Rachel Werther / Abigail A Westburg / Daniel P Bies / Stephanie I Walter / Yvette A Luyten / Richard D Morgan / Barry L Stoddard / Brett K Kaiser /
Abstract: Bacteriophage exclusion ('BREX') systems are multi-protein complexes encoded by a variety of bacteria and archaea that restrict phage by an unknown mechanism. One BREX factor, termed BrxL, has been ...Bacteriophage exclusion ('BREX') systems are multi-protein complexes encoded by a variety of bacteria and archaea that restrict phage by an unknown mechanism. One BREX factor, termed BrxL, has been noted to display sequence similarity to various AAA+ protein factors including Lon protease. In this study we describe multiple CryoEM structures of BrxL that demonstrate it to be a chambered, ATP-dependent DNA binding protein. The largest BrxL assemblage corresponds to a dimer of heptamers in the absence of bound DNA, versus a dimer of hexamers when DNA is bound in its central pore. The protein displays DNA-dependent ATPase activity, and ATP binding promotes assembly of the complex on DNA. Point mutations within several regions of the protein-DNA complex alter one or more in vitro behaviors and activities, including ATPase activity and ATP-dependent association with DNA. However, only the disruption of the ATPase active site fully eliminates phage restriction, indicating that other mutations can still complement BrxL function within the context of an otherwise intact BREX system. BrxL displays significant structural homology to MCM subunits (the replicative helicase in archaea and eukaryotes), implying that it and other BREX factors may collaborate to disrupt initiation of phage DNA replication.
History
DepositionSep 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 17, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease Lon-related BREX system protein BrxL
B: Protease Lon-related BREX system protein BrxL
C: Protease Lon-related BREX system protein BrxL
D: Protease Lon-related BREX system protein BrxL
E: Protease Lon-related BREX system protein BrxL
F: Protease Lon-related BREX system protein BrxL
G: Protease Lon-related BREX system protein BrxL
H: Protease Lon-related BREX system protein BrxL
I: Protease Lon-related BREX system protein BrxL
J: Protease Lon-related BREX system protein BrxL
K: Protease Lon-related BREX system protein BrxL
L: Protease Lon-related BREX system protein BrxL
O: DNA (64-MER)
P: DNA (63-MER)


Theoretical massNumber of molelcules
Total (without water)947,60614
Polymers947,60614
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Protease Lon-related BREX system protein BrxL


Mass: 75702.555 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter sp. NEB 394 (bacteria) / Gene: brxL, HUK62_18280 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7H8SL14
#2: DNA chain DNA (64-MER)


Mass: 19689.639 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (63-MER)


Mass: 19485.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: complex of walkerB mutant of BrxL with random sequence of DNA fragments
Type: COMPLEX
Details: 12 strands of KrxL E280Q mutant bound to short random sequence DNA fragments.
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.950 MDa / Experimental value: NO
Source (natural)Organism: Acinetobacter (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8 / Details: 20 mM TrisHCl, 150 mM NaCl
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: The sample was mono-disperse
Specimen supportDetails: 40 / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 275 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 12100 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 70 K
Image recordingAverage exposure time: 2 sec. / Electron dose: 30 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: DIRECT ELECTRON DE-10 (5k x 4k) / Num. of grids imaged: 2
Image scansMovie frames/image: 50 / Used frames/image: 1-49

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
1cryoSPARC3.3.2particle selection
4cryoSPARC3.3.2CTF correction
10cryoSPARC3.3.2initial Euler assignment
11cryoSPARC3.3.2final Euler assignment
13cryoSPARC3.3.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3241183
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 229430 / Num. of class averages: 4 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00367297
ELECTRON MICROSCOPYf_angle_d0.60591367
ELECTRON MICROSCOPYf_dihedral_angle_d14.9779950
ELECTRON MICROSCOPYf_chiral_restr0.04310029
ELECTRON MICROSCOPYf_plane_restr0.00511346

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