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- PDB-8zir: DUF4297-HerA complex -

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Basic information

Entry
Database: PDB / ID: 8zir
TitleDUF4297-HerA complex
Components
  • DUF4297
  • HerA
KeywordsIMMUNE SYSTEM / Complex / nuclease
Function / homologyADENOSINE-5'-TRIPHOSPHATE
Function and homology information
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.08 Å
AuthorsYu, Y. / Chen, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Mol Cell / Year: 2025
Title: DUF4297 and HerA form abortosome to mediate bacterial immunity against phage infection.
Authors: Dongmei Tang / Ting Liu / Yijun Chen / Zixuan Zhu / Hao Chen / Qiang Chen / Yamei Yu /
Abstract: Immune receptors form higher-order complexes known as inflammasomes in animals and resistosomes in plants to mediate immune signaling. Here, we report a similar bacterial protein complex, DUF4297- ...Immune receptors form higher-order complexes known as inflammasomes in animals and resistosomes in plants to mediate immune signaling. Here, we report a similar bacterial protein complex, DUF4297-HerA, which induces abortive infection to mediate anti-phage immunity by coupling nuclease and ATPase activities. Therefore, we name this defense system "Hailibu" after a hunter in a popular folk tale who sacrifices himself to save his village. Cryoelectron microscopy (cryo-EM) results reveal that DUF4297 and HerA assemble into a higher-order complex, reminiscent of apoptosome, inflammasome, or resistosome, which we refer to as an abortosome. By capturing cryo-EM structures of the pre-loading, DNA-loading, and DNA-transporting states during Hailibu abortosome processing of DNA, we propose that DNA substrates are loaded through the HerA hexamer, with adenosine triphosphate (ATP) hydrolysis providing the energy to transport DNA substrates to the clustered DUF4297 Cap4 nuclease domains for degradation. This study demonstrates the existence of analogous multiprotein complexes in innate immunity across the kingdoms of life.
History
DepositionMay 14, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Mar 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.0Mar 12, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.1Apr 9, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first / _em_admin.last_update
Revision 1.2Jul 2, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 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
A: DUF4297
B: DUF4297
C: DUF4297
D: DUF4297
E: DUF4297
F: DUF4297
G: DUF4297
H: DUF4297
I: DUF4297
J: DUF4297
K: DUF4297
L: DUF4297
M: HerA
N: HerA
O: HerA
P: HerA
Q: HerA
R: HerA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)953,53224
Polymers951,93718
Non-polymers1,5946
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
DUF4297


Mass: 45444.953 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein
HerA


Mass: 67766.328 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


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


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
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: HerA-DUF4297 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Agrobacterium tumefaciens (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
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: 5899 nm / Nominal defocus min: 328 nm
Image recordingElectron dose: 65.58 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 158570 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.009104075
ELECTRON MICROSCOPYf_angle_d0.843187282
ELECTRON MICROSCOPYf_dihedral_angle_d8.22442156
ELECTRON MICROSCOPYf_chiral_restr0.0568130
ELECTRON MICROSCOPYf_plane_restr0.00415393

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