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- EMDB-37923: Cryo-EM structure of DSR2 (H171A)-tube-NAD+ (partial) complex -

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Basic information

Entry
Database: EMDB / ID: EMD-37923
TitleCryo-EM structure of DSR2 (H171A)-tube-NAD+ (partial) complex
Map data
Sample
  • Complex: CryoEM structure of DSR2 (H171A)-Tube NAD+ (half) complex
    • Protein or peptide: SIR2-like domain-containing protein
    • Protein or peptide: Bacillus phage SPR Tube protein
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
KeywordsPhage defense proteins / ANTIVIRAL PROTEIN
Function / homologySIR2-like domain / SIR2-like domain / DHS-like NAD/FAD-binding domain superfamily / Uncharacterized protein / SIR2-like domain-containing protein
Function and homology information
Biological speciesBacillus subtilis (bacteria) / Bacillus phage SPR (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsZhang JT / Jia N / Liu XY
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
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
DepositionOct 30, 2023-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37923.png

Downloads & links

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Map

FileDownload / File: emd_37923.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.827 Å
Density
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-3.3790545 - 4.9663877
Average (Standard dev.)-0.00007340166 (±0.08079953)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 446.58002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_37923_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Half map: #2

Fileemd_37923_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_37923_half_map_2.map
Projections & Slices
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Sample components

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Entire : CryoEM structure of DSR2 (H171A)-Tube NAD+ (half) complex

EntireName: CryoEM structure of DSR2 (H171A)-Tube NAD+ (half) complex
Components
  • Complex: CryoEM structure of DSR2 (H171A)-Tube NAD+ (half) complex
    • Protein or peptide: SIR2-like domain-containing protein
    • Protein or peptide: Bacillus phage SPR Tube protein
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

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Supramolecule #1: CryoEM structure of DSR2 (H171A)-Tube NAD+ (half) complex

SupramoleculeName: CryoEM structure of DSR2 (H171A)-Tube NAD+ (half) complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Bacillus subtilis (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 (bacteria)
Molecular weightTheoretical: 118.568727 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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 KVAGDFRKGF 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

UniProtKB: SIR2-like domain-containing protein

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Macromolecule #2: Bacillus phage SPR Tube protein

MacromoleculeName: Bacillus phage SPR Tube protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacillus phage SPR (virus)
Molecular weightTheoretical: 29.304701 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #3: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 3 / Number of copies: 4 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM / Nicotinamide adenine dinucleotide

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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 KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 85495

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