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- EMDB-35978: Structure of HerA-Sir2 complex from Escherichia coli Nezha system -

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Basic information

Entry
Database: EMDB / ID: EMD-35978
TitleStructure of HerA-Sir2 complex from Escherichia coli Nezha system
Map datamrc-map
Sample
  • Complex: HerA-Sir2
    • Protein or peptide: SIR2-like domain-containing protein
    • Protein or peptide: Nucleoside triphosphate hydrolase
  • Ligand: [(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
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
Keywordsdefense system HerA Sir2 / IMMUNE SYSTEM
Function / homologyHelicase HerA, central domain / Helicase HerA, central domain / SIR2-like domain / SIR2-like domain / hydrolase activity / P-loop containing nucleoside triphosphate hydrolase / SIR2-like domain-containing protein / Nucleoside triphosphate hydrolase
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsChen Q / Yu Y
Funding support China, 1 items
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, 2023-
Header (metadata) releaseJan 3, 2024-
Map releaseJan 3, 2024-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35978.png

Downloads & links

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Map

FileDownload / File: emd_35978.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmrc-map
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 320 pix.
= 355.2 Å		1.11 Å/pix.
x 320 pix.
= 355.2 Å		1.11 Å/pix.
x 320 pix.
= 355.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.176
Minimum - Maximum-2.1500983 - 2.8305874
Average (Standard dev.)0.0034800565 (±0.0858596)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 355.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: mrc-map

Fileemd_35978_half_map_1.map
Annotationmrc-map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-mapA

Fileemd_35978_half_map_2.map
Annotationhalf-mapA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HerA-Sir2

EntireName: HerA-Sir2
Components
  • Complex: HerA-Sir2
    • Protein or peptide: SIR2-like domain-containing protein
    • Protein or peptide: Nucleoside triphosphate hydrolase
  • Ligand: [(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
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: HerA-Sir2

SupramoleculeName: HerA-Sir2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: SIR2-like domain-containing protein

MacromoleculeName: SIR2-like domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 46.817664 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSIYQGGNKL NEDDFRSHVY SLCQLDNVGV LLGAGASVGC GGKTMKDVWK SFKQNYPELL GALIDKYLLV SQIDSDNNLV NVELLIDEA TKFLSVAKTR RCEDEEEEFR KILSSLYKEV TKAALLTGEQ FREKNQGKKD AFKYHKELIS KLISNRQPGQ S APAIFTTN ...String:
MSIYQGGNKL NEDDFRSHVY SLCQLDNVGV LLGAGASVGC GGKTMKDVWK SFKQNYPELL GALIDKYLLV SQIDSDNNLV NVELLIDEA TKFLSVAKTR RCEDEEEEFR KILSSLYKEV TKAALLTGEQ FREKNQGKKD AFKYHKELIS KLISNRQPGQ S APAIFTTN YDLALEWAAE DLGIQLFNGF SGLHTRQFYP QNFDLAFRNV NAKGEARFGH YHAYLYKLHG SLTWYQNDSL TV NEVSASQ AYDEYINDII NKDDFYRGQH LIYPGANKYS HTIGFVYGEM FRRFGEFISK PQTALFINGF GFGDYHINRI ILG ALLNPS FHVVIYYPEL KEAITKVSKG GGSEAEKAIV TLKNMAFNQV TVVGGGSKAY FNSFVEHLPY PVLFPRDNIV DELV EAIAN LSKGEGNVPF

UniProtKB: SIR2-like domain-containing protein

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Macromolecule #2: Nucleoside triphosphate hydrolase

MacromoleculeName: Nucleoside triphosphate hydrolase / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 68.431992 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSLFKLTEIS AIGYVVGLEG ERIRINLHEG LQGRLASHRK GVSSVTQPGD LIGFDAGNIL VVARVTDMAF VEADKAHKAN VGTSDLADI PLRQIIAYAI GFVKRELNGY VFISEDWRLP ALGSSAVPLT SDFLNIIYSI DKEELPKAVE LGVDSRTKTV K IFASVDKL ...String:
MSLFKLTEIS AIGYVVGLEG ERIRINLHEG LQGRLASHRK GVSSVTQPGD LIGFDAGNIL VVARVTDMAF VEADKAHKAN VGTSDLADI PLRQIIAYAI GFVKRELNGY VFISEDWRLP ALGSSAVPLT SDFLNIIYSI DKEELPKAVE LGVDSRTKTV K IFASVDKL LSRHLAVLGS TGYGKSNFNA LLTRKVSEKY PNSRIVIFDI NGEYAQAFTG IPNVKHTILG ESPNVDSLEK KQ QKGELYS EEYYCYKKIP YQALGFAGLI KLLRPSDKTQ LPALRNALSA INRTHFKSRN IYLEKDDGET FLLYDDCRDT NQS KLAEWL DLLRRRRLKR TNVWPPFKSL ATLVAEFGCV AADRSNGSKR DAFGFSNVLP LVKIIQQLAE DIRFKSIVNL NGGG ELADG GTHWDKAMSD EVDYFFGKEK GQENDWNVHI VNMKNLAQDH APMLLSALLE MFAEILFRRG QERSYPTVLL LEEAH HYLR DPYAEIDSQI KAYERLAKEG RKFKCSLIVS TQRPSELSPT VLAMCSNWFS LRLTNERDLQ ALRYAMESGN EQILKQ ISG LPRGDAVAFG SAFNLPVRIS INQARPGPKS SDAVFSEEWA NCTELRC

UniProtKB: Nucleoside triphosphate hydrolase

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Macromolecule #3: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]ME...

MacromoleculeName: [(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
type: ligand / ID: 3 / Number of copies: 12 / Formula: AR6
Molecular weightTheoretical: 559.316 Da

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Macromolecule #4: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 4 / Number of copies: 5 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 590454
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
FSC plot (resolution estimation)

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