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- EMDB-39913: Local refinement of DSR2-tail tube-NAD+ complex -

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Basic information

Entry
Database: EMDB / ID: EMD-39913
TitleLocal refinement of DSR2-tail tube-NAD+ complex
Map data
Sample
  • Complex: DSR2-tail tube protein-NAD complex
KeywordsNADase / anti-phage defense / tail-tube protein / NAD / IMMUNE SYSTEM
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsWang R / Xu Q / Wu Z / Li J / Yang R / Shi Z / Li F
Funding support China, 3 items
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
DepositionApr 28, 2024-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateSep 11, 2024-
Current statusSep 11, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39913.png

Downloads & links

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Map

FileDownload / File: emd_39913.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 360 pix.
= 432. Å		1.2 Å/pix.
x 360 pix.
= 432. Å		1.2 Å/pix.
x 360 pix.
= 432. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.3787457 - 2.182494
Average (Standard dev.)-0.00020070926 (±0.0474566)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 432.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39913_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39913_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DSR2-tail tube protein-NAD complex

EntireName: DSR2-tail tube protein-NAD complex
Components
  • Complex: DSR2-tail tube protein-NAD complex

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Supramolecule #1: DSR2-tail tube protein-NAD complex

SupramoleculeName: DSR2-tail tube protein-NAD complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Bacillus subtilis (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: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
100.0 mMNaClsodium chloride
0.5 mMTCEPtris(2-carboxyethyl)phosphine

Details: 20 mM HEPES pH 7.5, 100 mM NaCl, 0.5 mM TCEP
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK I
Details10mg/ml

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 57864
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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