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Yorodumi- PDB-8dk1: CryoEM structure of JetABC (head construct) from Pseudomonas aeru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dk1 | |||||||||
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Title | CryoEM structure of JetABC (head construct) from Pseudomonas aeruginosa PA14 | |||||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / Wadjet / Bacterial defense systems / JetA / JetB / JetC / Anti-plasmid defense system / EptA / EptB / EptC / MksB / MksE / MksF / SMC / DNA BINDING PROTEIN-DNA complex | |||||||||
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 / DUF3375 domain-containing protein / DUF4194 domain-containing protein / ATP synthase Function and homology information | |||||||||
Biological species | Pseudomonas aeruginosa PA14 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.95 Å | |||||||||
Authors | Deep, A. / Gu, Y. / Gao, Y. / Ego, K. / Herzik, M. / Zhou, H. / Corbett, K. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Mol Cell / Year: 2022 Title: The SMC-family Wadjet complex protects bacteria from plasmid transformation by recognition and cleavage of closed-circular DNA. Authors: Amar Deep / Yajie Gu / Yong-Qi Gao / Kaori M Ego / Mark A Herzik / Huilin Zhou / Kevin D Corbett / Abstract: Self versus non-self discrimination is a key element of innate and adaptive immunity across life. In bacteria, CRISPR-Cas and restriction-modification systems recognize non-self nucleic acids through ...Self versus non-self discrimination is a key element of innate and adaptive immunity across life. In bacteria, CRISPR-Cas and restriction-modification systems recognize non-self nucleic acids through their sequence and their methylation state, respectively. Here, we show that the Wadjet defense system recognizes DNA topology to protect its host against plasmid transformation. By combining cryoelectron microscopy with cross-linking mass spectrometry, we show that Wadjet forms a complex similar to the bacterial condensin complex MukBEF, with a novel nuclease subunit similar to a type II DNA topoisomerase. Wadjet specifically cleaves closed-circular DNA in a reaction requiring ATP hydrolysis by the structural maintenance of chromosome (SMC) ATPase subunit JetC, suggesting that the complex could use DNA loop extrusion to sense its substrate's topology, then specifically activate the nuclease subunit JetD to cleave plasmid DNA. Overall, our data reveal how bacteria have co-opted a DNA maintenance machine to specifically recognize and destroy foreign DNAs through topology sensing. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dk1.cif.gz | 490.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dk1.ent.gz | 394.9 KB | Display | PDB format |
PDBx/mmJSON format | 8dk1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dk1_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8dk1_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8dk1_validation.xml.gz | 74.9 KB | Display | |
Data in CIF | 8dk1_validation.cif.gz | 111.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/8dk1 ftp://data.pdbj.org/pub/pdb/validation_reports/dk/8dk1 | HTTPS FTP |
-Related structure data
Related structure data | 27480MC 7tilC 8dk2C 8dk3C 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: 59233.500 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PA14 (bacteria) / Gene: PA14_03250 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2ZJP9 #2: Protein | Mass: 70675.375 Da / Num. of mol.: 2 / Mutation: L783A, E1022Q Source method: isolated from a genetically manipulated source Details: JetC head domain is constructed through a glycine serine link replacing two long coiled-coils. Additional mutations are: E1022Q, L783A.,JetC head domain is constructed through a glycine ...Details: JetC head domain is constructed through a glycine serine link replacing two long coiled-coils. Additional mutations are: E1022Q, L783A.,JetC head domain is constructed through a glycine serine link replacing two long coiled-coils. Additional mutations are: E1022Q, L783A. Source: (gene. exp.) Pseudomonas aeruginosa PA14 (bacteria) / Gene: IPC1494_27645, IPC1595_14260, IPC607_32065 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8G4Z850 #3: Protein | Mass: 27537.037 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PA14 (bacteria) / Gene: PA14_03265 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2ZL66 |
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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: Reconstituted JetABC head construct / Type: COMPLEX Details: A Pseudomonas aeruginosa protein complex involved in anti-plasmid defense system. Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||||||||||||
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Molecular weight | Value: 0.369 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) | Organism: Pseudomonas aeruginosa PA14 (bacteria) | ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 Details: Prepared using deionized water and filtered sterilized. | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 54.1 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: cryoSPARC / Version: 3.3.1 / Category: CTF correction | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 130904 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
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