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- PDB-8j4u: Structure of HerA-Sir2 complex from Escherichia coli Nezha system -

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Basic information

Entry
Database: PDB / ID: 8j4u
TitleStructure of HerA-Sir2 complex from Escherichia coli Nezha system
Components
  • Nucleoside triphosphate hydrolase
  • SIR2-like domain-containing protein
KeywordsIMMUNE SYSTEM / defense system HerA Sir2
Function / homology
Function and homology information


Helicase HerA, central domain / Helicase HerA, central domain / SIR2-like domain / SIR2-like domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Chem-AR6 / SIR2-like domain-containing protein / Nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsChen, Q. / Yu, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32270761, 31741027 China
CitationJournal: Mol Cell / Year: 2023
Title: Multiple enzymatic activities of a Sir2-HerA system cooperate for anti-phage defense.
Authors: Dongmei Tang / Yijun Chen / Hao Chen / Tingting Jia / Qiang Chen / Yamei Yu /
Abstract: In response to the persistent exposure to phage infection, bacteria have evolved diverse antiviral defense mechanisms. In this study, we report a bacterial two-component defense system consisting of ...In response to the persistent exposure to phage infection, bacteria have evolved diverse antiviral defense mechanisms. In this study, we report a bacterial two-component defense system consisting of a Sir2 NADase and a HerA helicase. Cryo-electron microscopy reveals that Sir2 and HerA assemble into a ∼1 MDa supramolecular octadecamer. Unexpectedly, this complex exhibits various enzymatic activities, including ATPase, NADase, helicase, and nuclease, which work together in a sophisticated manner to fulfill the antiphage function. Therefore, we name this defense system "Nezha" after a divine warrior in Chinese mythology who employs multiple weapons to defeat enemies. Our findings demonstrate that Nezha could sense phage infections, self-activate to arrest cell growth, eliminate phage genomes, and subsequently deactivate to allow for cell recovery. Collectively, Nezha represents a paradigm of sophisticated and multifaceted strategies bacteria use to defend against viral infections.
History
DepositionApr 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release
Revision 1.0Jan 3, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 3, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.1Jun 18, 2025Group: Data collection / Derived calculations / Structure summary
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Revision 1.1Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / EM metadata
Group: Data processing / Experimental summary / Structure summary
Data content type: EM metadata / EM metadata / EM metadata / Category: em_admin / em_software / entity
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
I: SIR2-like domain-containing protein
J: SIR2-like domain-containing protein
K: SIR2-like domain-containing protein
L: SIR2-like domain-containing protein
M: Nucleoside triphosphate hydrolase
N: Nucleoside triphosphate hydrolase
O: Nucleoside triphosphate hydrolase
P: Nucleoside triphosphate hydrolase
Q: Nucleoside triphosphate hydrolase
R: Nucleoside triphosphate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)981,75636
Polymers972,40418
Non-polymers9,35218
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
SIR2-like domain-containing protein


Mass: 46817.664 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ERS139208_00135 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7B5N0T7
#2: Protein
Nucleoside triphosphate hydrolase


Mass: 68431.992 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ERS139208_00134 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A822U1Y5
#3: Chemical
ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#4: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / 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-Sir2 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
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: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 590454 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004130546
ELECTRON MICROSCOPYf_angle_d0.785234966
ELECTRON MICROSCOPYf_dihedral_angle_d9.01453265
ELECTRON MICROSCOPYf_chiral_restr0.0519860
ELECTRON MICROSCOPYf_plane_restr0.00419382

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