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- EMDB-39259: The tetramer Structure of DSR2-SPR with NAD -

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Basic information

Entry
Database: EMDB / ID: EMD-39259
TitleThe tetramer Structure of DSR2-SPR with NAD
Map dataAuthor stated: because of data quality issues, we cannot obtain high-resolution data, and the current resolution barely allows us to see the C and D chains.
Sample
  • Complex: The tetramer of DSR2-SPR with NAD
    • Protein or peptide: SIR2-like domain-containing protein
    • Protein or peptide: SPR
KeywordsSIR2 / NADase / SPR / tetramer / 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: 4.4 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_39259.png

Downloads & links

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Map

FileDownload / File: emd_39259.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAuthor stated: because of data quality issues, we cannot obtain high-resolution data, and the current resolution barely allows us to see the C and D chains.
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 460 pix.
= 381.8 Å		0.83 Å/pix.
x 460 pix.
= 381.8 Å		0.83 Å/pix.
x 460 pix.
= 381.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.024855902 - 2.1869195
Average (Standard dev.)0.0014952353 (±0.024831643)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 381.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_39259_additional_1.map
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Half map: #2

Fileemd_39259_half_map_1.map
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Half map: #1

Fileemd_39259_half_map_2.map
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Sample components

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Entire : The tetramer of DSR2-SPR with NAD

EntireName: The tetramer of DSR2-SPR with NAD
Components
  • Complex: The tetramer of DSR2-SPR with NAD
    • Protein or peptide: SIR2-like domain-containing protein
    • Protein or peptide: SPR

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Supramolecule #1: The tetramer of DSR2-SPR with NAD

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

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Macromolecule #1: SIR2-like domain-containing protein

MacromoleculeName: SIR2-like domain-containing protein / 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 D4G637.
Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis A29 (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: SPR

MacromoleculeName: SPR / 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: A0A162TY69.
Number of copies: 4 / 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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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: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49893
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-8ygp:
The tetramer Structure of DSR2-SPR with NAD

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