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- EMDB-45126: Apo HerA of HerA-Duf4297 supramolecular complex in anti-phage defense -

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Basic information

Entry
Database: EMDB / ID: EMD-45126
TitleApo HerA of HerA-Duf4297 supramolecular complex in anti-phage defense
Map dataDeepEmhancer version of cryosparc map
Sample
  • Complex: Homo-oligomeric hexamer HerA
    • Protein or peptide: ATP-binding protein
KeywordsComplex / topoisomerase / ATPase / ANTIVIRAL PROTEIN
Function / homologyHelicase HerA-like / Helicase HerA, central domain / Helicase HerA, central domain / P-loop containing nucleoside triphosphate hydrolase / ATP binding / ATP-binding protein
Function and homology information
Biological speciesBacillus sp. HMF5848 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsRish A / Fosuah E / Fu TM
Funding support United States, 2 items
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
DepositionMay 29, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45126.png

Downloads & links

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Map

FileDownload / File: emd_45126.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEmhancer version of cryosparc map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.45 Å/pix.
x 384 pix.
= 172.762 Å		0.45 Å/pix.
x 384 pix.
= 172.762 Å		0.45 Å/pix.
x 384 pix.
= 172.762 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.4499 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.042428195 - 1.9978547
Average (Standard dev.)0.007285171 (±0.054929785)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 172.7616 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: cryosparc refined map at 3.26A by fsc

Fileemd_45126_additional_1.map
Annotationcryosparc refined map at 3.26A by fsc
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_45126_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_45126_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Homo-oligomeric hexamer HerA

EntireName: Homo-oligomeric hexamer HerA
Components
  • Complex: Homo-oligomeric hexamer HerA
    • Protein or peptide: ATP-binding protein

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Supramolecule #1: Homo-oligomeric hexamer HerA

SupramoleculeName: Homo-oligomeric hexamer HerA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus sp. HMF5848 (bacteria)
Molecular weightTheoretical: 400 KDa

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Macromolecule #1: ATP-binding protein

MacromoleculeName: ATP-binding protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. HMF5848 (bacteria)
Molecular weightTheoretical: 67.182125 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKIGSVIESS PHSILVKIDT LKIFEKAKSA LQIGKYLKIQ EGNHNFVLCV IQNIKISTDK DEDIFILTVQ PVGIFKGEEF FQGNSMLPS PTEPVFLVED DILNKIFSNE KTKIFHLGNL AQNEEVSFTL DGDKFFSKHV AVVGSTGSGK SCAVAKILQN V VGINDARN ...String:
MKIGSVIESS PHSILVKIDT LKIFEKAKSA LQIGKYLKIQ EGNHNFVLCV IQNIKISTDK DEDIFILTVQ PVGIFKGEEF FQGNSMLPS PTEPVFLVED DILNKIFSNE KTKIFHLGNL AQNEEVSFTL DGDKFFSKHV AVVGSTGSGK SCAVAKILQN V VGINDARN INKSDKKNSH IIIFDIHSEY KSAFEIDKNE DFNLNYLDVE KLKLPYWLMN SEELETLFIE SNEQNSHNQV SQ FKRAVVL NKEKYNPEFK KITYDSPVYF NINEVFNYIY NLNEEVINKI EGEPSLPKLS NGELVENRQI YFNEKLEFTS SNT SKATKA SNGPFNGEFN RFLSRFETKL TDKRLEFLLL NQDVEENSKY RTEHFEDILK QFMGYLDRSN VSIIDLSGIP FEVL SITIS LISRLIFDFA FHYSKLQHQK DELNDIPFMI VCEEAHNYIP RTGGIEFKAA KKSIERIAKE GRKYGLSLMV VSQRP SEVS DTILSQCNNF INLRLTNIND QNYIKNLLPD NSRSISEILP TLGAGECLVV GDSTPIPSIV KLELPNPEPR SQSIKF HKK WSESWRTPSF EEVIMRWRKE NG

UniProtKB: ATP-binding protein

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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: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 718668
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9c1o:
Apo HerA of HerA-Duf4297 supramolecular complex in anti-phage defense

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