Skip to main content

 8WKS | pdb_00008wks

Cryo-EM structure of DSR2-TUBE complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.58 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8WKS

This is version 1.0 of the entry. See complete history. 

Literature

Molecular basis of bacterial DSR2 anti-phage defense and viral immune evasion.

Huang, J., Zhu, K., Gao, Y., Ye, F., Li, Z., Ge, Y., Liu, S., Yang, J., Gao, A.

(2024) Nat Commun 15: 3954-3954

  • DOI: https://doi.org/10.1038/s41467-024-48291-4
  • Primary Citation Related Structures: 
    8WKS, 8WKT, 8WKX

  • PubMed 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 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.


  • Organizational Affiliation: 
    • Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China. jfhuang@ibp.ac.cn.

Macromolecule Content 

  • Total Structure Weight: 590.97 kDa 
  • Atom Count: 36,899 
  • Modeled Residue Count: 4,459 
  • Deposited Residue Count: 5,072 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SIR2-like domain-containing protein
A, D, F, H
1,004Bacillus subtilis subsp. natto BEST195Mutation(s): 0 
Gene Names: BSNT_07056
UniProt
Find proteins for A0ABF7PGM4 (Bacillus subtilis subsp. natto (strain BEST195))
Explore A0ABF7PGM4 
Go to UniProtKB:  A0ABF7PGM4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ABF7PGM4
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
TUBE
B, C, E, G
264Siphoviridae sp. ct0106Mutation(s): 0 
Gene Names: B4122_1986, BJQ93_02798, J5227_09585
UniProt
Find proteins for A0AAE9G628 (Bacillus phage SPR)
Explore A0AAE9G628 
Go to UniProtKB:  A0AAE9G628
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AAE9G628
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.58 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-22
    Type: Initial release