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- EMDB-38397: Intact MAP of defence-associated sirtuin 2 (DSR2) H171A protein i... -

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Basic information

Entry
Database: EMDB / ID: EMD-38397
TitleIntact MAP of defence-associated sirtuin 2 (DSR2) H171A protein in complex with DSAD1 (DSR anti-defence 1)
Map data
Sample
  • Complex: DSR2 H171A in complex with DSAD1
Keywordsdefence-associated sirtuin 2 (DSR2) protein / Sir2 / DSAD1 (DSR anti-defence 1) / CELL INVASION
Biological speciesBacillus sp. DSM 5850 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.99 Å
AuthorsLi Y / Zhang H / Zheng Q / Wu Y / Li S
Funding support1 items
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 21, 2023-
Header (metadata) releaseOct 23, 2024-
Map releaseOct 23, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38397.png

Downloads & links

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Map

FileDownload / File: emd_38397.map.gz / Format: CCP4 / Size: 18.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
2.64 Å/pix.
x 170 pix.
= 448.8 Å		2.64 Å/pix.
x 170 pix.
= 448.8 Å		2.64 Å/pix.
x 170 pix.
= 448.8 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.64 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-1.5926065 - 3.599175
Average (Standard dev.)-0.003051591 (±0.13486741)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions170170170
Spacing170170170
CellA=B=C: 448.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38397_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

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Half map: #2

Fileemd_38397_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : DSR2 H171A in complex with DSAD1

EntireName: DSR2 H171A in complex with DSAD1
Components
  • Complex: DSR2 H171A in complex with DSAD1

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Supramolecule #1: DSR2 H171A in complex with DSAD1

SupramoleculeName: DSR2 H171A in complex with DSAD1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bacillus sp. DSM 5850 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.99 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 42050
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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