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- EMDB-39254: The dimer Structure of SPR-DSR2(CTD) complex -

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Basic information

Entry
Database: EMDB / ID: EMD-39254
TitleThe dimer Structure of SPR-DSR2(CTD) complex
Map data
Sample
  • Complex: The dimer of SPR-DSR2(CTD)
    • Protein or peptide: SPR
    • Protein or peptide: SIR2-like domain-containing protein
KeywordsSIR2 / NADase / dimer / HYDROLASE
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 A29 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.78 Å
AuthorsGao X / Zhu H / Cui S
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2025
Title: Activation of the bacterial defense-associated sirtuin system.
Authors: Kaixiang Zhu / Kun Shang / Linyue Wang / Xia Yu / Lei Hua / Weihe Zhang / Bo Qin / Jia Wang / Xiaopan Gao / Hongtao Zhu / Sheng Cui /
Abstract: The NADase activity of the defense-associated sirtuins (DSRs) is activated by the phage tail tube protein (TTP). Herein, we report cryo-EM structures of a free-state Bacillus subtilis DSR2 tetramer ...The NADase activity of the defense-associated sirtuins (DSRs) is activated by the phage tail tube protein (TTP). Herein, we report cryo-EM structures of a free-state Bacillus subtilis DSR2 tetramer and a fragment of the tetramer, a phage SPR tail tube, and two DSR2-TTP complexes. DSR2 contains an N-terminal SIR2 domain, a middle domain (MID) and a C-terminal domain (CTD). The DSR2 CTD harbors the α-solenoid tandem-repeats like the HEAT-repeat proteins. DSR2 assembles into a tetramer with four SIR2 clustered at the center, and two intertwined MID-CTD chains flank the SIR2 core. SPR TTPs self-assemble into a tube-like complex. Upon DSR2 binding, the D1 domain of SPR TTP is captured between the HEAT-repeats domains of DSR2, which conflicts with TTPs self-assembly. Binding of TTPs induces conformational changes in DSR2 tetramer, resulting in increase of the NAD pocket volume in SIR2, thus activates the NADase activity and leads to cellular NAD depletion.
History
DepositionFeb 26, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39254.png

Downloads & links

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Map

FileDownload / File: emd_39254.map.gz / Format: CCP4 / Size: 83.7 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.)
0.83 Å/pix.
x 280 pix.
= 232.4 Å		0.83 Å/pix.
x 280 pix.
= 232.4 Å		0.83 Å/pix.
x 280 pix.
= 232.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.031959362 - 2.3051822
Average (Standard dev.)0.0027143282 (±0.036709506)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 232.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39254_msk_1.map
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Half map: #1

Fileemd_39254_half_map_1.map
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Half map: #2

Fileemd_39254_half_map_2.map
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Sample components

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Entire : The dimer of SPR-DSR2(CTD)

EntireName: The dimer of SPR-DSR2(CTD)
Components
  • Complex: The dimer of SPR-DSR2(CTD)
    • Protein or peptide: SPR
    • Protein or peptide: SIR2-like domain-containing protein

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Supramolecule #1: The dimer of SPR-DSR2(CTD)

SupramoleculeName: The dimer of SPR-DSR2(CTD) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus subtilis A29 (bacteria)

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Macromolecule #1: SPR

MacromoleculeName: SPR / type: protein_or_peptide / ID: 1
Details: Sequence reference for Bacillus subtilis A29 (2508883) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID: A0A162TY69.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis A29 (bacteria)
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 #2: SIR2-like domain-containing protein

MacromoleculeName: SIR2-like domain-containing protein / type: protein_or_peptide / ID: 2
Details: Sequence reference for Bacillus subtilis A29 (2508883) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID D4G637.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis A29 (bacteria)
Molecular weightTheoretical: 84.14568 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ENKFITKDDE VIDYIYGKIS PLFALQYIRK IDLKHVFEYD YHFEVNGTVV RHKNKGFGYM ERFFELKESC DERSKLSKKQ YERFNALFN FFEKNGVICM AKDAGTLNTS IEINSLAYHG KYDVMKKFIE EQSVSIEDDY KKAFFLACLG RWEESYDLYS N IILNSIDE ...String:
ENKFITKDDE VIDYIYGKIS PLFALQYIRK IDLKHVFEYD YHFEVNGTVV RHKNKGFGYM ERFFELKESC DERSKLSKKQ YERFNALFN FFEKNGVICM AKDAGTLNTS IEINSLAYHG KYDVMKKFIE EQSVSIEDDY KKAFFLACLG RWEESYDLYS N IILNSIDE SNGCVYYLSQ INRYRIYQSI TQAVTQFNGL GLLTFGRHYK PFTDEFLARI EREMTNFNID DLFNGMPFEF QK KYKILEF LSDNQFLYDD TVKLFELTNK VRSEMSEGSY SFGMSSDIVV LLRLYDNLRF LYENCLWSVS FHEFHQYIRN SMS LLIEKA EYERTRDIDE LGFSFFGKKS GFFMEYYDFV NISRHFKIDD IKNLERSCSI DKIRFGEQEK IEEYLVGIAE EITK QFSAN GMNVVFYTQF ISEAKAALYF AKYVKLSEEG LGKIVKALLF YFPERDLDIG KRYVWLERLT KCNELPKSII SIIDD FLVL QAEKHIDQNY SEVSSNGLYS RDYGALIKHF EKNFISKRLS EITLCLTQDK QKQIDFLFKL LPLLSTNAKS HLLSFK SVE NINDLMNGIR IGLIDEFTPE HEELIIEYLE TRKVNYIVEK EKGIQTFSSN DYMSTFGIWY FLEEINNSKM EEFIGMD DQ YDFFVDPENF DYKKFIPSWL KNYNDKLLGK IAGNKHMKHH VIEVLKERVK NSNDKRYLEI LMNYFI

UniProtKB: SIR2-like domain-containing protein

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 66.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.5 µm / Calibrated defocus min: 1.8 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 368518
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8ygk:
The dimer Structure of SPR-DSR2(CTD) complex

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