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Open data
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Basic information
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Title | Cryo-EM structure of DSR2-DSAD1 (partial) complex | |||||||||
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![]() | Phage defense proteins / ANTIVIRAL PROTEIN | |||||||||
Function / homology | Uncharacterized protein![]() | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.49 Å | |||||||||
![]() | Zhang JT / Jia N / Liu XY | |||||||||
Funding support | 1 items
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![]() | ![]() Title: Structural basis for phage-mediated activation and repression of bacterial DSR2 anti-phage defense system. Authors: Jun-Tao Zhang / Xiao-Yu Liu / Zhuolin Li / Xin-Yang Wei / Xin-Yi Song / Ning Cui / Jirui Zhong / Hongchun Li / Ning Jia / ![]() Abstract: Silent information regulator 2 (Sir2) proteins typically catalyze NAD-dependent protein deacetylation. The recently identified bacterial Sir2 domain-containing protein, defense-associated sirtuin 2 ...Silent information regulator 2 (Sir2) proteins typically catalyze NAD-dependent protein deacetylation. The recently identified bacterial Sir2 domain-containing protein, defense-associated sirtuin 2 (DSR2), recognizes the phage tail tube and depletes NAD to abort phage propagation, which is counteracted by the phage-encoded DSR anti-defense 1 (DSAD1), but their molecular mechanisms remain unclear. Here, we determine cryo-EM structures of inactive DSR2 in its apo form, DSR2-DSAD1 and DSR2-DSAD1-NAD, as well as active DSR2-tube and DSR2-tube-NAD complexes. DSR2 forms a tetramer with its C-terminal sensor domains (CTDs) in two distinct conformations: CTD or CTD. Monomeric, rather than oligomeric, tail tube proteins preferentially bind to CTD and activate Sir2 for NAD hydrolysis. DSAD1 binding to CTD allosterically inhibits tube binding and tube-mediated DSR2 activation. Our findings provide mechanistic insight into DSR2 assembly, tube-mediated DSR2 activation, and DSAD1-mediated inhibition and NAD substrate catalysis in bacterial DSR2 anti-phage defense systems. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 229.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.2 KB 15.2 KB | Display Display | ![]() |
Images | ![]() | 46.7 KB | ||
Masks | ![]() | 244.1 MB | ![]() | |
Filedesc metadata | ![]() | 5.8 KB | ||
Others | ![]() ![]() | 226.5 MB 226.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8wyeMC ![]() 8wy8C ![]() 8wy9C ![]() 8wyaC ![]() 8wybC ![]() 8wycC ![]() 8wydC ![]() 8wyfC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 0.827 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: #1
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Density Histograms |
-Half map: #2
File | emd_37925_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : CryoEM structure of DSR2-DSAD1 (half) complex
Entire | Name: CryoEM structure of DSR2-DSAD1 (half) complex |
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Components |
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-Supramolecule #1: CryoEM structure of DSR2-DSAD1 (half) complex
Supramolecule | Name: CryoEM structure of DSR2-DSAD1 (half) complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: SIR2 family protein
Macromolecule | Name: SIR2 family protein / type: protein_or_peptide / ID: 1 / Details: WP_029317421.1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 118.635789 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MVKVDLESKR YGEKLKEVFL MLDNNVVECI KEITESSRNG KLVFFVGAGV STLSDYPQWW RLVDKYHEEL YGSPKKGNYS SDEYLRIPQ IFYNVKGEMA FDGILKDFFQ VDKPTNPIHD KILAMNPAHV ITTNYDNLID TACWKRGKYF SVISAEEDVA N ATSSRYLL ...String: MVKVDLESKR YGEKLKEVFL MLDNNVVECI KEITESSRNG KLVFFVGAGV STLSDYPQWW RLVDKYHEEL YGSPKKGNYS SDEYLRIPQ IFYNVKGEMA FDGILKDFFQ VDKPTNPIHD KILAMNPAHV ITTNYDNLID TACWKRGKYF SVISAEEDVA N ATSSRYLL KVHGDFRKGF KGENVVLKED DYLNYDQNYP LISNLMKTII ATHTIVFIGY GLGDYNINML LNWVRKLQKD SF HKPFFIR TDPSPIENET LIYYENKGLR IIDAASLIDS NEYDYLERYS AVMDLLIESQ ENKFITKDDE VIDYIYGKIS PLF ALQYIR KIDLKHVFEY DYHFEVNGTV VRHKNKGFGY MERFFELKES CDERSKLSKK QYERFNALFN FFEKNGVICM AKDA GTLNT SIEINSLAYH GKYDVMKKFI EEQSVSIEDD YKKAFFLACL GRWEESYDLY SNIILNSIDE SNGCVYYLSQ INRYR IYQS ITQAVTQFNG LGLLTFGRHY KPFTDEFLAR IEREMTNFNI DDLFNGMPFE FQKKYKILEF LSDNQFLYDD TVKLFE LTN KVRSEMSEGS YSFGMSSDIV VLLRLYDNLR FLYENCLWSV SFHEFHQYIR NSMSLLIEKA EYERTRDIDE LGFSFFG KK SGFFMEYYDF VNISRHFKID DIKNLERSCS IDKIRFGEQE KIEEYLVGIA EEITKQFSAN GMNVVFYTQF ISEAKAAL Y FAKYVKLSEE GLGKIVKALL FYFPERDLDI GKRYVWLERL TKCNELPKSI ISIIDDFLVL QAEKHIDQNY SEVSSNGLY SRDYGALIKH FEKNFISKRL SEITLCLTQD KQKQIDFLFK LLPLLSTNAK SHLLSFKSVE NINDLMNGIR IGLIDEFTPE HEELIIEYL ETRKVNYIVE KEKGIQTFSS NDYMSTFGIW YFLEEINNSK MEEFIGMDDQ YDFFVDPENF DYKKFIPSWL K NYNDKLLG KIAGNKHMKH HVIEVLKERV KNSNDKRYLE ILMNYFI |
-Macromolecule #2: Bacillus phage SPbeta DSAD1 protein
Macromolecule | Name: Bacillus phage SPbeta DSAD1 protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 16.587791 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MIEIFKDTGA THDLVYHSKI NTFVWDVEFD IVLSDSKELN KCYFVKCFNP YRINGKCDFA VSSIDIFSEG KRLLIENEFN FKITKAVHV ATSKDVTEIV LHLSERISSP FPIVKEVVYL DWSHPQFEKG GGSGGGSGGW SHPQFEK UniProtKB: Uncharacterized protein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 946024 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: RANDOM ASSIGNMENT |