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- EMDB-61299: Helical structure of EfAvs5(SIR2-STAND) -

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Basic information

Entry
Database: EMDB / ID: EMD-61299
TitleHelical structure of EfAvs5(SIR2-STAND)
Map data
Sample
  • Complex: EfAvs5(SIR2-STAND)
    • Protein or peptide: SIR2-like domain-containing protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsanti-phage / sir2 / STAND / IMMUNE SYSTEM
Function / homology: / Novel STAND NTPase 3 / SIR2-like domain / SIR2-like domain / P-loop containing nucleoside triphosphate hydrolase / SIR2-like domain-containing protein
Function and homology information
Biological speciesEscherichia fergusonii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWang Y / Zheng J
Funding support China, 1 items
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, 2024-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61299.png

Downloads & links

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Map

FileDownload / File: emd_61299.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 360 pix.
= 320.4 Å		0.89 Å/pix.
x 360 pix.
= 320.4 Å		0.89 Å/pix.
x 360 pix.
= 320.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.89 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.5878203 - 1.0179777
Average (Standard dev.)0.0021627657 (±0.026478276)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 320.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61299_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61299_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : EfAvs5(SIR2-STAND)

EntireName: EfAvs5(SIR2-STAND)
Components
  • Complex: EfAvs5(SIR2-STAND)
    • Protein or peptide: SIR2-like domain-containing protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: EfAvs5(SIR2-STAND)

SupramoleculeName: EfAvs5(SIR2-STAND) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia fergusonii (bacteria)
Molecular weightTheoretical: 800 KDa

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Macromolecule #1: SIR2-like domain-containing protein

MacromoleculeName: SIR2-like domain-containing protein / type: protein_or_peptide / ID: 1
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.
Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Escherichia fergusonii (bacteria)
Molecular weightTheoretical: 100.285055 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MDAMLNSLKL ANSANESISD ETYERLKRLI STGNAIVFVG AGFSKESINI IGSTPPLAKD LALQISNKS ANYLKEVGAD SHYIEEIKQC DDLMVASDFF LNNIPQKDEL LQLLKDNYTI KDVTQEQIDI FSMKWRRIYT T NYDNAIEL ...String:
MGSSHHHHHH SSGLVPRGSH MDAMLNSLKL ANSANESISD ETYERLKRLI STGNAIVFVG AGFSKESINI IGSTPPLAKD LALQISNKS ANYLKEVGAD SHYIEEIKQC DDLMVASDFF LNNIPQKDEL LQLLKDNYTI KDVTQEQIDI FSMKWRRIYT T NYDNAIEL SLIKSGKSVT PLTLEDAPNQ YKSAEDICLH INGRIERSKE SDLDSAIKLT TSSYLSPEQF LTSSWYRQFK AD IDNASAI VFLGYSMYDI DIQKIFFNDS SIKSKTFFIT REGTTKFQNY KLAMFGEVIN IGVNAFSHIA AKCIEESHQD KEV GLINSL ELYTPGEEHD EIRDNDIANF MIFGKVSDRY IDEVTLNDNM HDKIILREEV SKIIEHIETD NDILIASDLG NGKS IMTRM LMSKLSRKGY LCFYYLYNEF SFSKDIERLS KLGQKIVIFI DDYSNCIDDT RYAIENRKDN IQLVLTTRHF GYENT KQHL LTMDMSSFKT HSVDYLSDSE VDNFVHIVDH LGAWGEKAGL SRHEKLSELD ENARNQLSFL LLSILKSEAI QSRIRE ISN LALNDKEYKE TVFAILLLDV IGLPLVRSLI SDVAVNEKIY SAEFTENEGV KNLFIISNGM VKTKSSTLSR FLIANIF EH KYVVNQLLKV IEHLYVINKD AKDHRLQTLI TSLLRFSIIE KLLPQRRVEI NYFYEKVKHI IPNLINDPHF WVQYAMSM I PFKDYPSADR YLATAYSLAA RKDNYHTKNI DTQRARLHLL VSLTKTGNEA YLEFEAGDNL IRIIPNDIYK YRQVLRYRD IYEKVYPTFN AKQKVFYEHA IKRIIKESES PELVEDLTYK IGVNWLDKLR GNLKLIVENI QENRPKGKK

UniProtKB: SIR2-like domain-containing protein

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 8 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 8 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTRISTRIS
50.0 mMKClKCl
3.0 mMDTTDTT
5.0 mMMgCl2MgCl2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 77.0 K / Max: 77.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.1 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
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

Particle selectionNumber selected: 1392237
Startup modelType of model: NONE
Final reconstructionNumber classes used: 3 / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 228053
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

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

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