+Open data
-Basic information
Entry | Database: PDB / ID: 8k98 | ||||||
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Title | Cryo-EM structure of DSR2-TTP | ||||||
Components | (a protein) x 2 | ||||||
Keywords | ANTIVIRAL PROTEIN / cryo-EM structure of a protein | ||||||
Biological species | Bacillus halotolerans (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||
Authors | Zhang, H. / Li, Z. / Li, X.Z. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Insights into the modulation of bacterial NADase activity by phage proteins. Authors: Hang Yin / Xuzichao Li / Xiaoshen Wang / Chendi Zhang / Jiaqi Gao / Guimei Yu / Qiuqiu He / Jie Yang / Xiang Liu / Yong Wei / Zhuang Li / Heng Zhang / Abstract: The Silent Information Regulator 2 (SIR2) protein is widely implicated in antiviral response by depleting the cellular metabolite NAD. The defense-associated sirtuin 2 (DSR2) effector, a SIR2 domain- ...The Silent Information Regulator 2 (SIR2) protein is widely implicated in antiviral response by depleting the cellular metabolite NAD. The defense-associated sirtuin 2 (DSR2) effector, a SIR2 domain-containing protein, protects bacteria from phage infection by depleting NAD, while an anti-DSR2 protein (DSR anti-defense 1, DSAD1) is employed by some phages to evade this host defense. The NADase activity of DSR2 is unleashed by recognizing the phage tail tube protein (TTP). However, the activation and inhibition mechanisms of DSR2 are unclear. Here, we determine the cryo-EM structures of DSR2 in multiple states. DSR2 is arranged as a dimer of dimers, which is facilitated by the tetramerization of SIR2 domains. Moreover, the DSR2 assembly is essential for activating the NADase function. The activator TTP binding would trigger the opening of the catalytic pocket and the decoupling of the N-terminal SIR2 domain from the C-terminal domain (CTD) of DSR2. Importantly, we further show that the activation mechanism is conserved among other SIR2-dependent anti-phage systems. Interestingly, the inhibitor DSAD1 mimics TTP to trap DSR2, thus occupying the TTP-binding pocket and inhibiting the NADase function. Together, our results provide molecular insights into the regulatory mechanism of SIR2-dependent NAD depletion in antiviral immunity. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8k98.cif.gz | 348.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8k98.ent.gz | 272.1 KB | Display | PDB format |
PDBx/mmJSON format | 8k98.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8k98_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8k98_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8k98_validation.xml.gz | 56.8 KB | Display | |
Data in CIF | 8k98_validation.cif.gz | 83.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/8k98 ftp://data.pdbj.org/pub/pdb/validation_reports/k9/8k98 | HTTPS FTP |
-Related structure data
Related structure data | 36980MC 8k9aC 8w56C 8wknC 8xknC M: map data used to model this data C: citing same article (ref.) |
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-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 29304.701 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus halotolerans (bacteria) / Production host: Escherichia coli (E. coli) #2: Protein | Mass: 118635.789 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus halotolerans (bacteria) / Production host: Escherichia coli (E. coli) |
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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: cryo-EM structure of a protein / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Bacillus halotolerans (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
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 defocus max: 2500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20000 / Symmetry type: POINT | ||||||||||||||||||||||||
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