+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25913 | |||||||||
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Title | CryoEM structure of JetD from Pseudomonas aeruginosa | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Wadjet / Bacterial defense systems / JetD / Anti-plasmid defense system / EptD / MksG / Toprim domain / Nuclease / Topoisomerase / DNA BINDING PROTEIN | |||||||||
Function / homology | Uncharacterised conserved protein UCP028408 / Wadjet protein JetD, C-terminal / Domain of unknown function DUF3322 / Wadjet protein JetD, C-terminal / Uncharacterized protein conserved in bacteria N-term (DUF3322) / Uncharacterized protein Function and homology information | |||||||||
Biological species | Pseudomonas aeruginosa PA14 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Deep A / Gu Y | |||||||||
Funding support | United States, 2 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25913.map.gz | 169.5 MB | EMDB map data format | |
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Header (meta data) | emd-25913-v30.xml emd-25913.xml | 28 KB 28 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25913_fsc.xml | 15.5 KB | Display | FSC data file |
Images | emd_25913.png | 104.8 KB | ||
Filedesc metadata | emd-25913.cif.gz | 6.1 KB | ||
Others | emd_25913_additional_1.map.gz emd_25913_additional_2.map.gz emd_25913_additional_3.map.gz emd_25913_additional_4.map.gz emd_25913_additional_5.map.gz emd_25913_additional_6.map.gz emd_25913_half_map_1.map.gz emd_25913_half_map_2.map.gz | 318.3 MB 318.3 MB 170.2 MB 318.1 MB 318.1 MB 170 MB 318.7 MB 318.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25913 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25913 | HTTPS FTP |
-Validation report
Summary document | emd_25913_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_25913_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_25913_validation.xml.gz | 24.1 KB | Display | |
Data in CIF | emd_25913_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25913 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25913 | HTTPS FTP |
-Related structure data
Related structure data | 7tilMC 8dk1C 8dk2C 8dk3C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_25913.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.65 Å | ||||||||||||||||||||
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #6
File | emd_25913_additional_1.map | ||||||||||||
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-Additional map: #5
File | emd_25913_additional_2.map | ||||||||||||
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-Additional map: #4
File | emd_25913_additional_3.map | ||||||||||||
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-Additional map: #3
File | emd_25913_additional_4.map | ||||||||||||
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-Additional map: #2
File | emd_25913_additional_5.map | ||||||||||||
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-Additional map: #1
File | emd_25913_additional_6.map | ||||||||||||
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-Half map: #2
File | emd_25913_half_map_1.map | ||||||||||||
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-Half map: #1
File | emd_25913_half_map_2.map | ||||||||||||
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Density Histograms |
-Sample components
-Entire : JetD
Entire | Name: JetD |
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Components |
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-Supramolecule #1: JetD
Supramolecule | Name: JetD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: A Pseudomonas aeruginosa protein. |
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Source (natural) | Organism: Pseudomonas aeruginosa PA14 (bacteria) |
Molecular weight | Theoretical: 85.6 kDa/nm |
-Macromolecule #1: JetD
Macromolecule | Name: JetD / type: protein_or_peptide / ID: 1 Details: Pseudomonas aeruginosa PA14 JetD protein with N-terminal TEV cleavable 6XHis tag. Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas aeruginosa PA14 (bacteria) / Strain: UCBPP-PA14 |
Molecular weight | Theoretical: 45.132164 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKSSHHHHHH ENLYFQSNAK SPTDIGRNLA RQWQRSSVRL ERLLNPGSWP QSLNIGKPSA RLFTDNIQAV LRHVENWRSV NVGKVDWEP VSYRAGLAPI SLPMRWHLRS PSEWIAASDD PRVSQEYAQL EYLVEQVDSA FHTLLVAQRS LWLTRTPEEV V ATAQLATQ ...String: MKSSHHHHHH ENLYFQSNAK SPTDIGRNLA RQWQRSSVRL ERLLNPGSWP QSLNIGKPSA RLFTDNIQAV LRHVENWRSV NVGKVDWEP VSYRAGLAPI SLPMRWHLRS PSEWIAASDD PRVSQEYAQL EYLVEQVDSA FHTLLVAQRS LWLTRTPEEV V ATAQLATQ LAPGCAQGRP LRLLAEHGVD TKFFERNATL LTKLLDERFE GAASEQGLTT FLDAFEESSH WVLVVPLQPG LL PFKRLRL TTSELAETPL PGSRLLVVEN EQCVHLLPET LPDTLAVLGA GLDLHWLASA HLAGKQIGYW GDMDTWGLLM LAR ARLHQP AVEALLMEQE LFEQHSQGNT VVEPAKALES APPGLLADEA DFYRYLLVQE RGRLEQEYLP KAQVELAIRK WAR UniProtKB: Uncharacterized protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.10 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
Details: Prepared using deionized water and filtered strelized. | ||||||||||||
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 12 sec. | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 62.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-7til: |