+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37606 | |||||||||
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Title | Cryo-EM structure of DSR2-TUBE 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 / Uncharacterized protein / SIR2-like domain-containing protein Function and homology information | |||||||||
Biological species | Bacillus subtilis subsp. natto (strain BEST195) (bacteria) / Siphoviridae sp. ct0106 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.58 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_37606.map.gz | 307.1 MB | EMDB map data format | |
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Header (meta data) | emd-37606-v30.xml emd-37606.xml | 15.4 KB 15.4 KB | Display Display | EMDB header |
Images | emd_37606.png | 120.5 KB | ||
Filedesc metadata | emd-37606.cif.gz | 6.2 KB | ||
Others | emd_37606_half_map_1.map.gz emd_37606_half_map_2.map.gz | 301.7 MB 301.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37606 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37606 | HTTPS FTP |
-Validation report
Summary document | emd_37606_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_37606_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_37606_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | emd_37606_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37606 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37606 | HTTPS FTP |
-Related structure data
Related structure data | 8wksMC 8wktC 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_37606.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_37606_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37606_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : DSR2-TUBE
Entire | Name: DSR2-TUBE |
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Components |
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-Supramolecule #1: DSR2-TUBE
Supramolecule | Name: DSR2-TUBE / 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: 118.437539 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 VAGDFRKGFK 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: TUBE
Macromolecule | Name: TUBE / type: protein_or_peptide / ID: 2 Details: Sequence reference for Siphoviridae sp. ct0106 (tax id 2825290) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A162TY69. Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Siphoviridae sp. ct0106 (virus) |
Molecular weight | Theoretical: 29.304701 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKTVIQDTAD VYFKRKSDGK LVFTAEAQTA SFSQAISEEK LRGGIGNKPL YILKSEKEIN LTVKNAFFDL EWLAMTQGET IQEETKVKV FDREHGLIVD DTNKVTLKGK PVSDVTFYNK KGLTYKIAVS TDGTYTIPTA FAAAKDKLTA VYQIEKVGRR L AIKASKFS ...String: MKTVIQDTAD VYFKRKSDGK LVFTAEAQTA SFSQAISEEK LRGGIGNKPL YILKSEKEIN LTVKNAFFDL EWLAMTQGET IQEETKVKV FDREHGLIVD DTNKVTLKGK PVSDVTFYNK KGLTYKIAVS TDGTYTIPTA FAAAKDKLTA VYQIEKVGRR L AIKASKFS ERYEVEYRTI AYNPDTEEVY SDIYIQFPNV SPSGEFEMSL ENGNALAPEI KFEALADTDT DEMAVVIEAS RD ENTAAPV EDTTGSTQSS DLGGTTE UniProtKB: Uncharacterized protein |
-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 TALOS ARCTICA |
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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: 200 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 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 127766 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |