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- EMDB-38302: Cryo-EM structure of defence-associated sirtuin 2 (DSR2) H171A pr... -

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Basic information

Entry
Database: EMDB / ID: EMD-38302
TitleCryo-EM structure of defence-associated sirtuin 2 (DSR2) H171A protein in complex with DSR anti-defence 1(DSAD1)
Map data
Sample
  • Complex: DSR2 protein in complex with DSAD1
    • Complex: DSR2 H171A
      • Protein or peptide: DSR2(H171A)
    • Complex: DSAD1
      • Protein or peptide: DSAD1
KeywordsCryo-EM / defence-associated sirtuin (DSR)DSR2 / DSR anti-defence 1(DSAD1) / Phage invasion / CELL INVASION
Biological speciesBacillus sp. DSM 5850 (bacteria) / Phage #D (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsLi Y / Zhang H / Zheng Q / Wu Y / Li S
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2024
Title: Structural insights into activation mechanisms on NADase of the bacterial DSR2 anti-phage defense system.
Authors: Hong Zhang / Yu Li / Lanlan Li / Lifei Chen / Chunhua Zhu / Lifang Sun / Panpan Dong / Dingding Jing / Jinbo Yang / Lei Fu / Fangnan Xiao / Ningshao Xia / Shaowei Li / Qingbing Zheng / Yunkun Wu /
Abstract: As a sirtuin (SIR2) family protein, defense-associated sirtuin2 (DSR2) has been demonstrated to participate in bacterial anti-phage resistance via depleting nicotinamide adenine dinucleotide (NAD) of ...As a sirtuin (SIR2) family protein, defense-associated sirtuin2 (DSR2) has been demonstrated to participate in bacterial anti-phage resistance via depleting nicotinamide adenine dinucleotide (NAD) of infected cells, which can be activated by tail tube protein (TTP) and inhibited by DSR anti-defense 1 (DSAD1) of diverse phages. However, the regulating mechanism remains elusive. Here, we determined the cryo-electron microscopy structure of apo DSR2, as well as the respective complex structures with TTP and DSAD1. Structural analyses and biochemical studies reveal that DSR2 forms a tetramer with a SIR2 central core and two distinct conformations. Monomeric TTP preferentially binds to the closed conformation of DSR2, inducing conformational distortions on SIR2 tetramer assembly to activate its NADase activity. DSAD1 combines with the open conformation of DSR2, directly or allosterically inhibiting TTP activation on DSR2 NAD hydrolysis. Our findings decipher the detailed molecule mechanisms for DSR2 NADase activity regulation and lay a foundation for in-depth understanding of the DSR2 anti-phage defense system.
History
DepositionDec 13, 2023-
Header (metadata) releaseOct 23, 2024-
Map releaseOct 23, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38302.png

Downloads & links

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Map

FileDownload / File: emd_38302.map.gz / Format: CCP4 / Size: 347.6 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.)
0.65 Å/pix.
x 450 pix.
= 292.5 Å		0.65 Å/pix.
x 450 pix.
= 292.5 Å		0.65 Å/pix.
x 450 pix.
= 292.5 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.13074599 - 0.2980575
Average (Standard dev.)0.000026541828 (±0.0076043378)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 292.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_38302_additional_1.map
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Half map: #2

Fileemd_38302_half_map_1.map
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Half map: #1

Fileemd_38302_half_map_2.map
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Sample components

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Entire : DSR2 protein in complex with DSAD1

EntireName: DSR2 protein in complex with DSAD1
Components
  • Complex: DSR2 protein in complex with DSAD1
    • Complex: DSR2 H171A
      • Protein or peptide: DSR2(H171A)
    • Complex: DSAD1
      • Protein or peptide: DSAD1

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Supramolecule #1: DSR2 protein in complex with DSAD1

SupramoleculeName: DSR2 protein in complex with DSAD1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: DSR2 H171A

SupramoleculeName: DSR2 H171A / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Bacillus sp. DSM 5850 (bacteria)

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Supramolecule #3: DSAD1

SupramoleculeName: DSAD1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Phage #D (virus)

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Macromolecule #1: DSR2(H171A)

MacromoleculeName: DSR2(H171A) / type: protein_or_peptide / ID: 1 / Details: WP_029317421.1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. DSM 5850 (bacteria)
Molecular weightTheoretical: 118.568727 KDa
Recombinant expressionOrganism: Bacteria Latreille et al. 1825 (Bacteria stick insect)
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

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Macromolecule #2: DSAD1

MacromoleculeName: DSAD1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Phage #D (virus)
Molecular weightTheoretical: 13.239132 KDa
Recombinant expressionOrganism: Bacteria Latreille et al. 1825 (Bacteria stick insect)
SequenceString:
KDTGATHDLV YHSKINTFVW DVEFDIVLSD SKELNKCYFV KCFNPYRING KCDFAVSSID IFSEGKRLLI ENEFNFKITK AVHVATSKD VTEIVLHLSE RISSPFPIVK EVVYLD

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K3 (6k 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: 0.9 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 269385
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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