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- PDB-9c5x: Molecular basis for HerA-Duf supramolecular complex in anti-phage... -

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Basic information

Entry
Database: PDB / ID: 9c5x
TitleMolecular basis for HerA-Duf supramolecular complex in anti-phage defense - Assembly 3
Components
  • ATP-binding protein
  • DUF4297 domain-containing protein
KeywordsANTIVIRAL PROTEIN / Oligomerization domain / nuclease / topoisomerase
Function / homologyHelicase HerA-like / Helicase HerA, central domain / Helicase HerA, central domain / P-loop containing nucleoside triphosphate hydrolase / ATP binding / ATP-binding protein / DUF4297 domain-containing protein
Function and homology information
Biological speciesBacillus sp. HMF5848 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsRish, A.D. / Fu, T.M. / Fosuah, E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GR128399 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM144293- 01 United States
CitationJournal: Mol Cell / Year: 2025
Title: Architecture remodeling activates the HerA-DUF anti-phage defense system.
Authors: Anthony D Rish / Elizabeth Fosuah / Zhangfei Shen / Ila A Marathe / Vicki H Wysocki / Tian-Min Fu /
Abstract: Leveraging AlphaFold models and integrated experiments, we characterized the HerA-DUF4297 (DUF) anti-phage defense system, focusing on DUF's undefined biochemical functions. Guided by structure-based ...Leveraging AlphaFold models and integrated experiments, we characterized the HerA-DUF4297 (DUF) anti-phage defense system, focusing on DUF's undefined biochemical functions. Guided by structure-based genomic analyses, we found DUF homologs to be universally distributed across diverse bacterial immune systems. Notably, one such homolog, Cap4, is a nuclease. Inspired by this evolutionary clue, we tested DUF's nuclease activity and observed that DUF cleaves DNA substrates only when bound to its partner protein HerA. To dissect the mechanism of DUF activation, we determined the structures of DUF and HerA-DUF. Although DUF forms large oligomeric assemblies both alone and with HerA, oligomerization alone was insufficient to elicit nuclease activity. Instead, HerA binding induces a profound architecture remodeling that propagates throughout the complex. This remodeling reconfigures DUF into an active nuclease capable of robust DNA cleavage. Together, we highlight an architecture remodeling-driven mechanism that may inform the activation of other immune systems.
History
DepositionJun 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUF4297 domain-containing protein
B: DUF4297 domain-containing protein
C: DUF4297 domain-containing protein
D: DUF4297 domain-containing protein
E: DUF4297 domain-containing protein
F: DUF4297 domain-containing protein
G: DUF4297 domain-containing protein
H: DUF4297 domain-containing protein
I: DUF4297 domain-containing protein
J: DUF4297 domain-containing protein
K: DUF4297 domain-containing protein
L: DUF4297 domain-containing protein
M: ATP-binding protein
N: ATP-binding protein
O: ATP-binding protein
P: ATP-binding protein
Q: ATP-binding protein
R: ATP-binding protein


Theoretical massNumber of molelcules
Total (without water)1,019,06218
Polymers1,019,06218
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
DUF4297 domain-containing protein


Mass: 51330.734 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. HMF5848 (bacteria) / Gene: EJF36_01570 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A428J1H2
#2: Protein
ATP-binding protein


Mass: 67182.125 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. HMF5848 (bacteria) / Gene: EJF36_01575 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3R9P6E2
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: Supramolecular complex of HerA-Duf anti-phage defense system
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 1.02 MDa / Experimental value: YES
Source (natural)Organism: Bacillus sp. HMF5848 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
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: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 530769 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00246890
ELECTRON MICROSCOPYf_angle_d0.44463264
ELECTRON MICROSCOPYf_dihedral_angle_d3.8416030
ELECTRON MICROSCOPYf_chiral_restr0.0437044
ELECTRON MICROSCOPYf_plane_restr0.0038154

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