+Open data
-Basic information
Entry | Database: PDB / ID: 8wkx | ||||||
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Title | Cryo-EM structure of DSR2 | ||||||
Components | SIR2-like domain-containing protein | ||||||
Keywords | SURFACTANT PROTEIN / Anti-phage immune / NADase / Defense-associated sirtuin 2 / DSR2 / Phage tail tube protein / DSR Anti Defense 1 / DSAD1 / Bacteria-phage interaction | ||||||
Function / homology | SIR2-like domain / SIR2-like domain / DHS-like NAD/FAD-binding domain superfamily / SIR2-like domain-containing protein Function and homology information | ||||||
Biological species | Bacillus subtilis subsp. natto (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.15 Å | ||||||
Authors | Gao, A. / Huang, J. / Zhu, K. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Molecular basis of bacterial DSR2 anti-phage defense and viral immune evasion. Authors: Jiafeng Huang / Keli Zhu / Yina Gao / Feng Ye / Zhaolong Li / Yao Ge / Songqing Liu / Jing Yang / Ang Gao / Abstract: Defense-associated sirtuin 2 (DSR2) systems are widely distributed across prokaryotic genomes, providing robust protection against phage infection. DSR2 recognizes phage tail tube proteins and ...Defense-associated sirtuin 2 (DSR2) systems are widely distributed across prokaryotic genomes, providing robust protection against phage infection. DSR2 recognizes phage tail tube proteins and induces abortive infection by depleting intracellular NAD, a process that is counteracted by another phage-encoded protein, DSR Anti Defense 1 (DSAD1). Here, we present cryo-EM structures of Bacillus subtilis DSR2 in its apo, Tube-bound, and DSAD1-bound states. DSR2 assembles into an elongated tetramer, with four NADase catalytic modules clustered in the center and the regulatory-sensing modules distributed at four distal corners. Interestingly, monomeric Tube protein, rather than its oligomeric states, docks at each corner of the DSR2 tetramer to form a 4:4 DSR2-Tube assembly, which is essential for DSR2 NADase activity. DSAD1 competes with Tube for binding to DSR2 by occupying an overlapping region, thereby inhibiting DSR2 immunity. Thus, our results provide important insights into the assembly, activation and inhibition of the DSR2 anti-phage defense system. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wkx.cif.gz | 362.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wkx.ent.gz | 296.7 KB | Display | PDB format |
PDBx/mmJSON format | 8wkx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wkx_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8wkx_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8wkx_validation.xml.gz | 68.4 KB | Display | |
Data in CIF | 8wkx_validation.cif.gz | 98.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/8wkx ftp://data.pdbj.org/pub/pdb/validation_reports/wk/8wkx | HTTPS FTP |
-Related structure data
Related structure data | 37610MC 8wksC 8wktC M: map data used to model this data C: citing same article (ref.) |
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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: 118635.789 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. natto (strain BEST195) (bacteria) Gene: BSNT_07056 / Production host: Escherichia coli (E. coli) / References: UniProt: D4G637 |
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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: DSR2 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Bacillus subtilis subsp. natto (strain BEST195) (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: FEI TITAN |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80223 / Symmetry type: POINT | ||||||||||||||||||||||||
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