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- PDB-9jap: Helical structure of EfAvs5(SIR2-STAND) -

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Basic information

Entry
Database: PDB / ID: 9jap
TitleHelical structure of EfAvs5(SIR2-STAND)
ComponentsSIR2-like domain-containing protein
KeywordsIMMUNE SYSTEM / anti-phage / sir2 / STAND
Function / homology: / Novel STAND NTPase 3 / SIR2-like domain / P-loop containing nucleoside triphosphate hydrolase / ADENOSINE-5'-TRIPHOSPHATE / SIR2 family protein
Function and homology information
Biological speciesEscherichia fergusonii (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWang, Y. / Zheng, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770068, 32070040 China
CitationJournal: Nat Commun / Year: 2025
Title: Filamentation activates bacterial Avs5 antiviral protein.
Authors: Yiqun Wang / Yuqing Tian / Xu Yang / Feng Yu / Jianting Zheng /
Abstract: Bacterial antiviral STANDs (Avs) are evolutionarily related to the nucleotide-binding oligomerization domain (NOD)-like receptors widely distributed in immune systems across animals and plants. ...Bacterial antiviral STANDs (Avs) are evolutionarily related to the nucleotide-binding oligomerization domain (NOD)-like receptors widely distributed in immune systems across animals and plants. EfAvs5, a type 5 Avs from Escherichia fergusonii, contains an N-terminal SIR2 effector domain, a NOD, and a C-terminal sensor domain, conferring protection against diverse phage invasions. Despite the established roles of SIR2 and STAND in prokaryotic and eukaryotic immunity, the mechanism underlying their collaboration remains unclear. Here we present cryo-EM structures of EfAvs5 filaments, elucidating the mechanisms of dimerization, filamentation, filament bundling, ATP binding, and NAD hydrolysis, all of which are crucial for anti-phage defense. The SIR2 and NOD domains engage in intra- and inter-dimer interaction to form an individual filament, while the outward C-terminal sensor domains contribute to bundle formation. Filamentation potentially stabilizes the dimeric SIR2 configuration, thereby activating the NADase activity of EfAvs5. Furthermore, we identify the nucleotide kinase gp1.7 of phage T7 as an activator of EfAvs5, demonstrating its ability to induce filamentation and NADase activity. Together, we uncover the filament assembly of Avs5 as a unique mechanism to switch enzyme activities and perform anti-phage defenses.
History
DepositionAug 25, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)806,53224
Polymers802,2808
Non-polymers4,25216
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


Mass: 100285.055 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: The protein belongs to Escherichia fergusonii, the NCBI Taxonomy ID is QML19490.1. Sequence reference for Escherichia fergusonii (564) is not available in UniProt at the time of biocuration. ...Details: The protein belongs to Escherichia fergusonii, the NCBI Taxonomy ID is QML19490.1. Sequence reference for Escherichia fergusonii (564) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID A0AA94GZI5.
Source: (gene. exp.) Escherichia fergusonii (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AA94GZI5
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: EfAvs5(SIR2-STAND) / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.8 MDa / Experimental value: YES
Source (natural)Organism: Escherichia fergusonii (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTRISTRIS1
250 mMKClKCl1
33 mMDTTDTT1
45 mMMgCl2MgCl21
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 289 K

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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: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 0.1 mm / C2 aperture diameter: 70 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 77 K / Temperature (min): 77 K
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum
Image scansMovie frames/image: 32

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Processing

EM software
IDNameVersionCategoryDetails
2SerialEM3.8.6image acquisition
9PHENIX1.20.1-4487model refinementautomated refinement using real-space maps
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1392237
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 228053 / Num. of class averages: 3 / Symmetry type: POINT
Atomic model buildingSpace: REAL

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