+Open data
-Basic information
Entry | Database: PDB / ID: 8bfn | ||||||
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Title | E. coli Wadjet JetABC dimer of dimers | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / SMC complexes / bacterial immunity / defense system / DNA loop extrusion / Wadjet / JetABCD / DNA cleavage / plasmid restriction / mksBEFG / mobile genetic elements / horizontal gene transfer / eptABCD / mukBEF | ||||||
Function / homology | Wadjet protein JetB / Domain of unknown function (DUF4194) / Protein of unknown function DUF3375 / Protein of unknown function (DUF3375) / P-loop containing nucleoside triphosphate hydrolase / ADENOSINE-5'-DIPHOSPHATE / DUF4194 domain-containing protein / ATP synthase / DUF3375 family protein Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.52 Å | ||||||
Authors | Roisne-Hamelin, F. / Beckert, B. / Myasnikov, A. / Li, Y. / Gruber, S. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Mol Cell / Year: 2022 Title: DNA-measuring Wadjet SMC ATPases restrict smaller circular plasmids by DNA cleavage. Authors: Hon Wing Liu / Florian Roisné-Hamelin / Bertrand Beckert / Yan Li / Alexander Myasnikov / Stephan Gruber / Abstract: Structural maintenance of chromosome (SMC) complexes fold DNA by loop extrusion to support chromosome segregation and genome maintenance. Wadjet systems (JetABCD/MksBEFG/EptABCD) are derivative SMC ...Structural maintenance of chromosome (SMC) complexes fold DNA by loop extrusion to support chromosome segregation and genome maintenance. Wadjet systems (JetABCD/MksBEFG/EptABCD) are derivative SMC complexes with roles in bacterial immunity against selfish DNA. Here, we show that JetABCD restricts circular plasmids with an upper size limit of about 100 kb, whereas a linear plasmid evades restriction. Purified JetABCD complexes cleave circular DNA molecules, regardless of the DNA helical topology; cleavage is DNA sequence nonspecific and depends on the SMC ATPase. A cryo-EM structure reveals a distinct JetABC dimer-of-dimers geometry, with the two SMC dimers facing in opposite direction-rather than the same as observed with MukBEF. We hypothesize that JetABCD is a DNA-shape-specific endonuclease and propose the "total extrusion model" for DNA cleavage exclusively when extrusion of an entire plasmid has been completed by a JetABCD complex. Total extrusion cannot be achieved on the larger chromosome, explaining how self-DNA may evade processing. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bfn.cif.gz | 769.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bfn.ent.gz | 609.1 KB | Display | PDB format |
PDBx/mmJSON format | 8bfn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bfn_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8bfn_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 8bfn_validation.xml.gz | 157.2 KB | Display | |
Data in CIF | 8bfn_validation.cif.gz | 224.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/8bfn ftp://data.pdbj.org/pub/pdb/validation_reports/bf/8bfn | HTTPS FTP |
-Related structure data
Related structure data | 16020MC 8as8C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 124562.938 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: C9160_20650 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / References: UniProt: A0A4T5T6V2 #2: Protein | Mass: 28020.416 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: BvCmsKKP036_00455 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / References: UniProt: A0A4C9B499 #3: Protein | Mass: 63350.883 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: GF4-3 / Gene: WP_171460373 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / References: UniProt: A0A4V3QHV5 #4: Chemical | ChemComp-ADP / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: JetABC(D) / Type: COMPLEX Details: E. coli JetABCD was purified by gel filtration. Note that JetD is not visible in the map. Entity ID: #1-#3 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Escherichia coli (E. coli) / Strain: GF4-3 |
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: BL21(DE3) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 283 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
EM software | Name: RELION / Version: 4 / Category: classification |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37333 / Symmetry type: POINT |