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- PDB-8ygn: The Dimer Structure of DSR2-SPR with NAD -

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Basic information

Entry
Database: PDB / ID: 8ygn
TitleThe Dimer Structure of DSR2-SPR with NAD
Components
  • SIR2-like domain-containing protein
  • SPR
KeywordsHYDROLASE / SPR / SIR2 / NADase / dimer
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.27 Å
AuthorsGao, X. / Zhu, H. / Cui, S.
Funding support1items
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, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: SPR
C: SPR
A: SIR2-like domain-containing protein
B: SIR2-like domain-containing protein
E: SIR2-like domain-containing protein
F: SIR2-like domain-containing protein


Theoretical massNumber of molelcules
Total (without water)532,8846
Polymers532,8846
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein SPR


Mass: 29304.701 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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.
Source: (gene. exp.) Bacillus subtilis A29 (bacteria) / Gene: B4122_1986, J5227_09585 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A162TY69
#2: Protein
SIR2-like domain-containing protein


Mass: 118568.727 Da / Num. of mol.: 4 / Mutation: H171A
Source method: isolated from a genetically manipulated source
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.
Source: (gene. exp.) Bacillus subtilis A29 (bacteria) / Gene: BSNT_07056 / Production host: Escherichia coli (E. coli) / References: UniProt: D4G637
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The dimer of DSR2-SPR with NAD / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Bacillus subtilis A29 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1800 nm / Calibrated defocus min: 1800 nm / Calibrated defocus max: 2500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 66 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14482 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00323769
ELECTRON MICROSCOPYf_angle_d0.65932063
ELECTRON MICROSCOPYf_dihedral_angle_d5.4413094
ELECTRON MICROSCOPYf_chiral_restr0.0423422
ELECTRON MICROSCOPYf_plane_restr0.0054111

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