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- PDB-8y3y: The Cryo-EM structure of anti-phage defense associated DSR2 tetra... -

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Basic information

Entry
Database: PDB / ID: 8y3y
TitleThe Cryo-EM structure of anti-phage defense associated DSR2 tetramer bound with two DSAD1 inhibitors (opposite side)
Components
  • DSR anti-defence 1
  • SIR2-like domain-containing protein
KeywordsIMMUNOSUPPRESSANT / NADase / anti-phage defense / complex / immune evasion
Function / homologySIR2-like domain / SIR2-like domain / DHS-like NAD/FAD-binding domain superfamily / : / SIR2-like domain-containing protein
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsWang, R.W. / Xu, Q. / Wu, Z.X. / Li, J.L. / Shi, Z.B. / Li, F.X.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32370742 China
National Natural Science Foundation of China (NSFC)32271264 China
National Natural Science Foundation of China (NSFC)32200129 China
CitationJournal: Nat Commun / Year: 2024
Title: The structural basis of the activation and inhibition of DSR2 NADase by phage proteins.
Authors: Ruiwen Wang / Qi Xu / Zhuoxi Wu / Jialu Li / Hao Guo / Tianzhui Liao / Yuan Shi / Ling Yuan / Haishan Gao / Rong Yang / Zhubing Shi / Faxiang Li /
Abstract: DSR2, a Sir2 domain-containing protein, protects bacteria from phage infection by hydrolyzing NAD. The enzymatic activity of DSR2 is triggered by the SPR phage tail tube protein (TTP), while ...DSR2, a Sir2 domain-containing protein, protects bacteria from phage infection by hydrolyzing NAD. The enzymatic activity of DSR2 is triggered by the SPR phage tail tube protein (TTP), while suppressed by the SPbeta phage-encoded DSAD1 protein, enabling phages to evade the host defense. However, the molecular mechanisms of activation and inhibition of DSR2 remain elusive. Here, we report the cryo-EM structures of apo DSR2, DSR2-TTP-NAD and DSR2-DSAD1 complexes. DSR2 assembles into a head-to-head tetramer mediated by its Sir2 domain. The C-terminal helical regions of DSR2 constitute four partner-binding cavities with opened and closed conformation. Two TTP molecules bind to two of the four C-terminal cavities, inducing conformational change of Sir2 domain to activate DSR2. Furthermore, DSAD1 competes with the activator for binding to the C-terminal cavity of DSR2, effectively suppressing its enzymatic activity. Our results provide the mechanistic insights into the DSR2-mediated anti-phage defense system and DSAD1-dependent phage immune evasion.
History
DepositionJan 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 11, 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: SIR2-like domain-containing protein
C: DSR anti-defence 1
D: SIR2-like domain-containing protein
E: SIR2-like domain-containing protein
F: DSR anti-defence 1


Theoretical massNumber of molelcules
Total (without water)502,2896
Polymers502,2896
Non-polymers00
Water00
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: 118635.789 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSNT_07056 / Production host: Escherichia coli B (bacteria) / References: UniProt: D4G637
#2: Protein DSR anti-defence 1


Mass: 13872.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yotI, CFD21_19895, NRS6116_11285, NRS6202_09785 / Production host: Escherichia coli B (bacteria) / References: UniProt: A0A9P1J8U5

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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: Complex of DSR2 tetramer and two DSAD1 inhibitors (opposite side)
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Bacillus subtilis (bacteria)
Source (recombinant)Organism: Escherichia coli B (bacteria)
Buffer solutionpH: 7.5 / Details: 20 mM HEPES pH 7.5, 100 mM NaCl, 0.5 mM TCEP
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 13000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.11.1_2575: / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91205 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00734350
ELECTRON MICROSCOPYf_angle_d1.08146282
ELECTRON MICROSCOPYf_dihedral_angle_d8.06520474
ELECTRON MICROSCOPYf_chiral_restr0.0594944
ELECTRON MICROSCOPYf_plane_restr0.0075890

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