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- PDB-8zc9: The Cryo-EM structure of DSR2-Tail tube-NAD+ complex -

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Basic information

Entry
Database: PDB / ID: 8zc9
TitleThe Cryo-EM structure of DSR2-Tail tube-NAD+ complex
Components
  • SIR2-like domain-containing protein
  • tail tube protein
KeywordsIMMUNE SYSTEM / NADase / anti-phage defense / tail-tube protein / NAD
Function / homologySIR2-like domain / SIR2-like domain / DHS-like NAD/FAD-binding domain superfamily / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Uncharacterized protein / SIR2-like domain-containing protein
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsWang, R. / Xu, Q. / Wu, Z. / Li, J. / Yang, R. / Shi, Z. / Li, F.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32370742 China
National Natural Science Foundation of China (NSFC)32271264 China
National Natural Science Foundation of China (NSFC)32200129 China
CitationJournal: Nat Commun / Year: 2024
Title: The structural basis of the activation and inhibition of DSR2 NADase by phage proteins.
Authors: Ruiwen Wang / Qi Xu / Zhuoxi Wu / Jialu Li / Hao Guo / Tianzhui Liao / Yuan Shi / Ling Yuan / Haishan Gao / Rong Yang / Zhubing Shi / Faxiang Li /
Abstract: DSR2, a Sir2 domain-containing protein, protects bacteria from phage infection by hydrolyzing NAD. The enzymatic activity of DSR2 is triggered by the SPR phage tail tube protein (TTP), while ...DSR2, a Sir2 domain-containing protein, protects bacteria from phage infection by hydrolyzing NAD. The enzymatic activity of DSR2 is triggered by the SPR phage tail tube protein (TTP), while suppressed by the SPbeta phage-encoded DSAD1 protein, enabling phages to evade the host defense. However, the molecular mechanisms of activation and inhibition of DSR2 remain elusive. Here, we report the cryo-EM structures of apo DSR2, DSR2-TTP-NAD and DSR2-DSAD1 complexes. DSR2 assembles into a head-to-head tetramer mediated by its Sir2 domain. The C-terminal helical regions of DSR2 constitute four partner-binding cavities with opened and closed conformation. Two TTP molecules bind to two of the four C-terminal cavities, inducing conformational change of Sir2 domain to activate DSR2. Furthermore, DSAD1 competes with the activator for binding to the C-terminal cavity of DSR2, effectively suppressing its enzymatic activity. Our results provide the mechanistic insights into the DSR2-mediated anti-phage defense system and DSAD1-dependent phage immune evasion.
History
DepositionApr 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: SIR2-like domain-containing protein
A: SIR2-like domain-containing protein
C: tail tube protein
E: SIR2-like domain-containing protein
D: SIR2-like domain-containing protein
F: tail tube protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)535,53810
Polymers532,8846
Non-polymers2,6544
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
SIR2-like domain-containing protein / DSR2


Mass: 118568.727 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The sequence of organism Bacillus subtilis is not available, replaced by D4G637 temporarily.
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSNT_07056 / Production host: Escherichia coli B (bacteria) / References: UniProt: D4G637
#2: Protein tail tube protein


Mass: 29304.701 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: J5227_09585 / Production host: Escherichia coli B (bacteria) / References: UniProt: A0A162TY69
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
Has ligand of interestY

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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: DSR2-tail tube protein-NAD+ complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Bacillus subtilis (bacteria)
Source (recombinant)Organism: Escherichia coli B (bacteria)
Buffer solutionpH: 7.5 / Details: 20 mM HEPES pH 7.5, 100 mM NaCl, 0.5 mM TCEP
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidHEPES1
2100 mMsodium chlorideNaCl1
30.5 mMtris(2-carboxyethyl)phosphineTCEP1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 10mg/ml
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 %

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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 magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: NONE
Particle selectionNum. of particles selected: 3383
3D reconstructionResolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57864 / Symmetry type: POINT
Atomic model buildingB value: 116
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 126.31 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002636054
ELECTRON MICROSCOPYf_angle_d0.559248594
ELECTRON MICROSCOPYf_chiral_restr0.0395168
ELECTRON MICROSCOPYf_plane_restr0.00386186
ELECTRON MICROSCOPYf_dihedral_angle_d5.87874718

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