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- EMDB-37607: Cryo-EM structure of DSR2-DSAD1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-37607
TitleCryo-EM structure of DSR2-DSAD1 complex
Map data
Sample
  • Complex: DSR2-DSAD1
    • Protein or peptide: SIR2-like domain-containing protein
    • Protein or peptide: SPbeta prophage-derived uncharacterized protein YotI
KeywordsAnti-phage immune / NADase / Defense-associated sirtuin 2 / DSR2 / Phage tail tube protein / DSR Anti Defense 1 / DSAD1 / Bacteria-phage interaction / STRUCTURAL PROTEIN
Function / homologySIR2-like domain / SIR2-like domain / DHS-like NAD/FAD-binding domain superfamily / symbiont-mediated suppression of host innate immune response / SIR2-like domain-containing protein / SPbeta prophage-derived DSR anti-defense 1
Function and homology information
Biological speciesBacillus subtilis subsp. natto (strain BEST195) (bacteria) / Caudoviricetes (bacterial and archaeal viruses with head-tail morphology)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.86 Å
AuthorsGao A / Huang J / Zhu K
Funding support1 items
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, 2023-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37607.png

Downloads & links

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Map

FileDownload / File: emd_37607.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 520 pix.
= 540.8 Å		1.04 Å/pix.
x 520 pix.
= 540.8 Å		1.04 Å/pix.
x 520 pix.
= 540.8 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.70643383 - 1.532958
Average (Standard dev.)-0.00019815369 (±0.039199453)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions520520520
Spacing520520520
CellA=B=C: 540.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37607_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Histogram (log scale)

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Half map: #1

Fileemd_37607_half_map_2.map
Projections & Slices
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Sample components

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Entire : DSR2-DSAD1

EntireName: DSR2-DSAD1
Components
  • Complex: DSR2-DSAD1
    • Protein or peptide: SIR2-like domain-containing protein
    • Protein or peptide: SPbeta prophage-derived uncharacterized protein YotI

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Supramolecule #1: DSR2-DSAD1

SupramoleculeName: DSR2-DSAD1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus subtilis subsp. natto (strain BEST195) (bacteria)

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Macromolecule #1: SIR2-like domain-containing protein

MacromoleculeName: SIR2-like domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. natto (strain BEST195) (bacteria)
Molecular weightTheoretical: 118.504602 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: VKVDLESKRY GEKLKEVFLM LDNNVVECIK EITESSRNGK LVFFVGAGVS TLSDYPQWWR LVDKYHEELY GSPKKGNYSS DEYLRIPQI FYNVKGEMAF DGILKDFFQV DKPTNPIHDK ILAMNPAHVI TTNYDNLIDT ACWKRGKYFS VISAEEDVAN A TSSRYLLK ...String:
VKVDLESKRY GEKLKEVFLM LDNNVVECIK EITESSRNGK LVFFVGAGVS TLSDYPQWWR LVDKYHEELY GSPKKGNYSS DEYLRIPQI FYNVKGEMAF DGILKDFFQV DKPTNPIHDK ILAMNPAHVI TTNYDNLIDT ACWKRGKYFS VISAEEDVAN A TSSRYLLK VHGDFRKGFK GENVVLKEDD YLNYDQNYPL ISNLMKTIIA THTIVFIGYG LGDYNINMLL NWVRKLQKDS FH KPFFIRT DPSPIENETL IYYENKGLRI IDAASLIDSN EYDYLERYSA VMDLLIESQE NKFITKDDEV IDYIYGKISP LFA LQYIRK IDLKHVFEYD YHFEVNGTVV RHKNKGFGYM ERFFELKESC DERSKLSKKQ YERFNALFNF FEKNGVICMA KDAG TLNTS IEINSLAYHG KYDVMKKFIE EQSVSIEDDY KKAFFLACLG RWEESYDLYS NIILNSIDES NGCVYYLSQI NRYRI YQSI TQAVTQFNGL GLLTFGRHYK PFTDEFLARI EREMTNFNID DLFNGMPFEF QKKYKILEFL SDNQFLYDDT VKLFEL TNK VRSEMSEGSY SFGMSSDIVV LLRLYDNLRF LYENCLWSVS FHEFHQYIRN SMSLLIEKAE YERTRDIDEL GFSFFGK KS GFFMEYYDFV NISRHFKIDD IKNLERSCSI DKIRFGEQEK IEEYLVGIAE EITKQFSANG MNVVFYTQFI SEAKAALY F AKYVKLSEEG LGKIVKALLF YFPERDLDIG KRYVWLERLT KCNELPKSII SIIDDFLVLQ AEKHIDQNYS EVSSNGLYS RDYGALIKHF EKNFISKRLS EITLCLTQDK QKQIDFLFKL LPLLSTNAKS HLLSFKSVEN INDLMNGIRI GLIDEFTPEH EELIIEYLE TRKVNYIVEK EKGIQTFSSN DYMSTFGIWY FLEEINNSKM EEFIGMDDQY DFFVDPENFD YKKFIPSWLK N YNDKLLGK IAGNKHMKHH VIEVLKERVK NSNDKRYLEI LMNYFI

UniProtKB: SIR2-like domain-containing protein

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Macromolecule #2: SPbeta prophage-derived uncharacterized protein YotI

MacromoleculeName: SPbeta prophage-derived uncharacterized protein YotI / type: protein_or_peptide / ID: 2
Details: Sequence reference for Caudoviricetes (tax id 2731619) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id Q796A8.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Caudoviricetes (bacterial and archaeal viruses with head-tail morphology)
Molecular weightTheoretical: 13.87293 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MIEIFKDTGA THDLVYHSKI NTFVWDVEFD IVLSDSKELN KCYFVKCFNP YRINGKCDFA VSSIDIFSEG KRLLIENEFN FKITKAVHV ATSKDVTEIV LHLSERISSP FPIVKEVVYL D

UniProtKB: SPbeta prophage-derived DSR anti-defense 1

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k 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: 1.2 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 105782
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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