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- PDB-8xff: Cryo-EM structure of defence-associatedsirtuin 2 (DSR2) H171A pro... -

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Basic information

Entry
Database: PDB / ID: 8xff
TitleCryo-EM structure of defence-associatedsirtuin 2 (DSR2) H171A protein in complex with SPR phage tail tube protein
Components
  • DSR2(H171A)
  • SPR tail tube protein
KeywordsCELL INVASION / Cryo-EM / defence-associated sirtuin (DSR)DSR2 / SPR phage tail tube / Phage invasion
Biological speciesPhage #D (virus)
Bacillus sp. DSM 5850 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsLi, Y. / Zhang, H. / Zheng, Q. / Wu, Y. / Li, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2024
Title: Structural insights into activation mechanisms on NADase of the bacterial DSR2 anti-phage defense system.
Authors: Hong Zhang / Yu Li / Lanlan Li / Lifei Chen / Chunhua Zhu / Lifang Sun / Panpan Dong / Dingding Jing / Jinbo Yang / Lei Fu / Fangnan Xiao / Ningshao Xia / Shaowei Li / Qingbing Zheng / Yunkun Wu /
Abstract: As a sirtuin (SIR2) family protein, defense-associated sirtuin2 (DSR2) has been demonstrated to participate in bacterial anti-phage resistance via depleting nicotinamide adenine dinucleotide (NAD) of ...As a sirtuin (SIR2) family protein, defense-associated sirtuin2 (DSR2) has been demonstrated to participate in bacterial anti-phage resistance via depleting nicotinamide adenine dinucleotide (NAD) of infected cells, which can be activated by tail tube protein (TTP) and inhibited by DSR anti-defense 1 (DSAD1) of diverse phages. However, the regulating mechanism remains elusive. Here, we determined the cryo-electron microscopy structure of apo DSR2, as well as the respective complex structures with TTP and DSAD1. Structural analyses and biochemical studies reveal that DSR2 forms a tetramer with a SIR2 central core and two distinct conformations. Monomeric TTP preferentially binds to the closed conformation of DSR2, inducing conformational distortions on SIR2 tetramer assembly to activate its NADase activity. DSAD1 combines with the open conformation of DSR2, directly or allosterically inhibiting TTP activation on DSR2 NAD hydrolysis. Our findings decipher the detailed molecule mechanisms for DSR2 NADase activity regulation and lay a foundation for in-depth understanding of the DSR2 anti-phage defense system.
History
DepositionDec 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: SPR tail tube protein
A: DSR2(H171A)
B: DSR2(H171A)
D: DSR2(H171A)
E: DSR2(H171A)


Theoretical massNumber of molelcules
Total (without water)503,5805
Polymers503,5805
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 SPR tail tube protein


Mass: 29304.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phage #D (virus)
Production host: Bacteria Latreille et al. 1825 (Bacteria stick insect)
#2: Protein
DSR2(H171A)


Mass: 118568.727 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: WP_029317421.1 / Source: (gene. exp.) Bacillus sp. DSM 5850 (bacteria) / Production host: Bacteria Latreille et al., 1825
Has protein modificationN

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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

Component
IDNameTypeEntity IDParent-IDSource
1DSR2 H171A protein in complex with SPR phage tail tubeCOMPLEXall0MULTIPLE SOURCES
2SPR tail tube proteinCOMPLEX#11RECOMBINANT
3DSR2 H171ACOMPLEX#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Phage #D (virus)77920
33Bacillus sp. DSM 5850 (bacteria)126787
Source (recombinant)Organism: Bacteria Latreille et al. 1825 (Bacteria stick insect)
Buffer solutionpH: 7.4
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: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 102635 / Symmetry type: POINT

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