+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37607 | |||||||||
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Title | Cryo-EM structure of DSR2-DSAD1 complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Anti-phage immune / NADase / Defense-associated sirtuin 2 / DSR2 / Phage tail tube protein / DSR Anti Defense 1 / DSAD1 / Bacteria-phage interaction / STRUCTURAL PROTEIN | |||||||||
Function / homology | SIR2-like domain / SIR2-like domain / DHS-like NAD/FAD-binding domain superfamily / SIR2-like domain-containing protein / SPbeta prophage-derived uncharacterized protein YotI Function and homology information | |||||||||
Biological species | Bacillus subtilis subsp. natto (strain BEST195) (bacteria) / Caudoviricetes (bacterial and archaeal viruses with head-tail morphology) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.86 Å | |||||||||
Authors | Gao A / Huang J / Zhu K | |||||||||
Funding support | 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37607.map.gz | 506.5 MB | EMDB map data format | |
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Header (meta data) | emd-37607-v30.xml emd-37607.xml | 15.3 KB 15.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_37607_fsc.xml | 17.2 KB | Display | FSC data file |
Images | emd_37607.png | 85.3 KB | ||
Filedesc metadata | emd-37607.cif.gz | 6.1 KB | ||
Others | emd_37607_half_map_1.map.gz emd_37607_half_map_2.map.gz | 498.2 MB 498.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37607 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37607 | HTTPS FTP |
-Validation report
Summary document | emd_37607_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_37607_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_37607_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | emd_37607_validation.cif.gz | 35.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37607 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37607 | HTTPS FTP |
-Related structure data
Related structure data | 8wktMC 8wksC 8wkxC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_37607.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_37607_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37607_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : DSR2-DSAD1
Entire | Name: DSR2-DSAD1 |
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Components |
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-Supramolecule #1: DSR2-DSAD1
Supramolecule | Name: DSR2-DSAD1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Bacillus subtilis subsp. natto (strain BEST195) (bacteria) |
-Macromolecule #1: SIR2-like domain-containing protein
Macromolecule | Name: SIR2-like domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus subtilis subsp. natto (strain BEST195) (bacteria) |
Molecular weight | Theoretical: 118.504602 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #2: SPbeta prophage-derived uncharacterized protein YotI
Macromolecule | Name: 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 |
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Source (natural) | Organism: Caudoviricetes (bacterial and archaeal viruses with head-tail morphology) |
Molecular weight | Theoretical: 13.87293 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MIEIFKDTGA THDLVYHSKI NTFVWDVEFD IVLSDSKELN KCYFVKCFNP YRINGKCDFA VSSIDIFSEG KRLLIENEFN FKITKAVHV ATSKDVTEIV LHLSERISSP FPIVKEVVYL D UniProtKB: SPbeta prophage-derived uncharacterized protein YotI |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm |