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Open data
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Basic information
Entry | Database: PDB / ID: 8wy8 | ||||||
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Title | Cryo-EM structure of DSR2 apo complex | ||||||
![]() | SIR2 family protein | ||||||
![]() | ANTIVIRAL PROTEIN / Phage defense proteins | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
![]() | Zhang, J.T. / Jia, N. / Liu, X.Y. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural basis for phage-mediated activation and repression of bacterial DSR2 anti-phage defense system. Authors: Jun-Tao Zhang / Xiao-Yu Liu / Zhuolin Li / Xin-Yang Wei / Xin-Yi Song / Ning Cui / Jirui Zhong / Hongchun Li / Ning Jia / ![]() Abstract: Silent information regulator 2 (Sir2) proteins typically catalyze NAD-dependent protein deacetylation. The recently identified bacterial Sir2 domain-containing protein, defense-associated sirtuin 2 ...Silent information regulator 2 (Sir2) proteins typically catalyze NAD-dependent protein deacetylation. The recently identified bacterial Sir2 domain-containing protein, defense-associated sirtuin 2 (DSR2), recognizes the phage tail tube and depletes NAD to abort phage propagation, which is counteracted by the phage-encoded DSR anti-defense 1 (DSAD1), but their molecular mechanisms remain unclear. Here, we determine cryo-EM structures of inactive DSR2 in its apo form, DSR2-DSAD1 and DSR2-DSAD1-NAD, as well as active DSR2-tube and DSR2-tube-NAD complexes. DSR2 forms a tetramer with its C-terminal sensor domains (CTDs) in two distinct conformations: CTD or CTD. Monomeric, rather than oligomeric, tail tube proteins preferentially bind to CTD and activate Sir2 for NAD hydrolysis. DSAD1 binding to CTD allosterically inhibits tube binding and tube-mediated DSR2 activation. Our findings provide mechanistic insight into DSR2 assembly, tube-mediated DSR2 activation, and DSAD1-mediated inhibition and NAD substrate catalysis in bacterial DSR2 anti-phage defense systems. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 756.6 KB | Display | ![]() |
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PDB format | ![]() | 624.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 107.5 KB | Display | |
Data in CIF | ![]() | 159.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 37919MC ![]() 8wy9C ![]() 8wyaC ![]() 8wybC ![]() 8wycC ![]() 8wydC ![]() 8wyeC ![]() 8wyfC M: map data used to model this data C: citing same article ( |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 118635.789 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: WP_029317421.1 / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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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 |
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Sample preparation
Component | Name: CryoEM structure of DSR2 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 59543 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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