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- PDB-8wks: Cryo-EM structure of DSR2-TUBE complex -

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Basic information

Entry
Database: PDB / ID: 8wks
TitleCryo-EM structure of DSR2-TUBE complex
Components
  • SIR2-like domain-containing protein
  • TUBE
KeywordsSTRUCTURAL PROTEIN / Anti-phage immune / NADase / Defense-associated sirtuin 2 / DSR2 / Phage tail tube protein / DSR Anti Defense 1 / DSAD1 / Bacteria-phage interaction
Function / homologySIR2-like domain / SIR2-like domain / DHS-like NAD/FAD-binding domain superfamily / Uncharacterized protein / SIR2-like domain-containing protein
Function and homology information
Biological speciesBacillus subtilis subsp. natto (bacteria)
Siphoviridae sp. ct0106 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsGao, A. / Huang, J. / Zhu, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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
DepositionSep 28, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SIR2-like domain-containing protein
B: TUBE
C: TUBE
D: SIR2-like domain-containing protein
E: TUBE
F: SIR2-like domain-containing protein
G: TUBE
H: SIR2-like domain-containing protein


Theoretical massNumber of molelcules
Total (without water)590,9698
Polymers590,9698
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
SIR2-like domain-containing protein


Mass: 118437.539 Da / Num. of mol.: 4
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
#2: Protein
TUBE


Mass: 29304.701 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Sequence reference for Siphoviridae sp. ct0106 (tax id 2825290) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A162TY69.
Source: (gene. exp.) Siphoviridae sp. ct0106 (virus) / Gene: B4122_1986, BJQ93_02798, J5227_09585 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A162TY69

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: DSR2-TUBE / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Bacillus subtilis subsp. natto (strain BEST195) (bacteria)645657
31Siphoviridae sp. ct0106 (virus)2825290
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 127766 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00237763
ELECTRON MICROSCOPYf_angle_d0.53850896
ELECTRON MICROSCOPYf_dihedral_angle_d4.0484891
ELECTRON MICROSCOPYf_chiral_restr0.0385411
ELECTRON MICROSCOPYf_plane_restr0.0036522

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