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- EMDB-60129: DUF4297-HerA complex with DNA and ATPgamaS -

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Basic information

Entry
Database: EMDB / ID: EMD-60129
TitleDUF4297-HerA complex with DNA and ATPgamaS
Map data
Sample
  • Complex: DUF4297-HerA-ATPgammaS
    • Protein or peptide: DUF4297
    • Protein or peptide: HerA
    • DNA: DNA (5'-D(P*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*A)-3')
    • DNA: DNA (5'-D(*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*T)-3')
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsComplex / Nuclease / ATPase / IMMUNE SYSTEM / IMMUNE SYSTEM-DNA complex
Biological speciesAgrobacterium tumefaciens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsYu Y / CHen Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) 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, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60129.png

Downloads & links

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Map

FileDownload / File: emd_60129.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 480 pix.
= 408. Å		0.85 Å/pix.
x 480 pix.
= 408. Å		0.85 Å/pix.
x 480 pix.
= 408. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0121
Minimum - Maximum-0.009063617 - 1.98352
Average (Standard dev.)0.0022573152 (±0.035945177)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 408.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_60129_additional_1.map
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Half map: #2

Fileemd_60129_half_map_1.map
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Half map: #1

Fileemd_60129_half_map_2.map
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Sample components

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Entire : DUF4297-HerA-ATPgammaS

EntireName: DUF4297-HerA-ATPgammaS
Components
  • Complex: DUF4297-HerA-ATPgammaS
    • Protein or peptide: DUF4297
    • Protein or peptide: HerA
    • DNA: DNA (5'-D(P*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*A)-3')
    • DNA: DNA (5'-D(*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*T)-3')
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: DUF4297-HerA-ATPgammaS

SupramoleculeName: DUF4297-HerA-ATPgammaS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Agrobacterium tumefaciens (bacteria)

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Macromolecule #1: DUF4297

MacromoleculeName: DUF4297 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium tumefaciens (bacteria)
Molecular weightTheoretical: 45.444953 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MARTAEYSIK GYLYQFLKYL SEILAAGDGA RITIEGAIED VDVIAAGLTT AVQCKYHEQA EKYTLGKIYK PILLMLEHFS KNSGTDLHV SYRLFCHFPG ESGTKALTKD DLETVLSTKG EVLRAIVARI DTSVDYEAFL DRFAIEFGPS AEDLQVAVLA S LKDKGFDP ...String:
MARTAEYSIK GYLYQFLKYL SEILAAGDGA RITIEGAIED VDVIAAGLTT AVQCKYHEQA EKYTLGKIYK PILLMLEHFS KNSGTDLHV SYRLFCHFPG ESGTKALTKD DLETVLSTKG EVLRAIVARI DTSVDYEAFL DRFAIEFGPS AEDLQVAVLA S LKDKGFDP DDIDAVIFPN AIQRIVDLAT RSDVNDRTVE PKTFLAGLRE VRRVTFTRWT RELATKGRMF SSLRKSLRSC LA HNSRWRV FVINPLTIEN FDDDIVRFIK AFVQRYSSKY LHSNPPLFML TGDYDLSVLQ KRLYDAGLRC ETGKVGGTDV IIK ELFRRP ILIRNPFRME FSLRLAKRDE VIGGPQRRPD ELFLINVADD EWKHEDVNVH GFKIERLSDL EYILQLRSDY A

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Macromolecule #2: HerA

MacromoleculeName: HerA / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium tumefaciens (bacteria)
Molecular weightTheoretical: 67.766328 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MPDLGTPIGS VTDSSPSLIR IEISSAEDFE KYKSMLGVGQ YLLVASGNNL YLLASITGVR ATHVERRSLG PSSEVHSEEG SDGISGNFR FQIDTQPIGT LSEDGEFSRG SHSLPVPTEY AYVTPPAVLE GIFSHQIKSP FALGTLGISP DIKLKIDGDR F FSKHVAVV ...String:
MPDLGTPIGS VTDSSPSLIR IEISSAEDFE KYKSMLGVGQ YLLVASGNNL YLLASITGVR ATHVERRSLG PSSEVHSEEG SDGISGNFR FQIDTQPIGT LSEDGEFSRG SHSLPVPTEY AYVTPPAVLE GIFSHQIKSP FALGTLGISP DIKLKIDGDR F FSKHVAVV GSTGSGKSCA VAKILQTAVG IESKANAHKA AQKNSHIVIF DIHAEYAAAF NLEAGEAFTL NLLGVDNLRL PY WLMNAQE LEQIFIESNE HNSHNQISQF RHAVVRNKCK HNPTLTNLSF DTPVYFSIDE VVTYLENMNN EVIGKLAGEG KPK LANETL VSDRDELYFD AVQSFIVASQ AAATKASNGP FNGEFDRMIL RLHTRLADPR LQFLFYPKKE DGEDLATGDF ADVV RQFVG YMTKSNVSII DLSGIPFEVL SIVVSLISRM IFDFGFHYSK NRHVGGAVSD VPILVVCEEA HNYLPRSGGA AYDAS RKSI ERIAKEGRKY GVTLMVVSQR PSEVSETIFS QCSNFISLRL TNAVDQTYVK SLLPDLSAGL GDLLPNLAQG EFLIVG DAP LMPTVGHFAL PVPEPHSRSV NYLQEWNSGW RHVDFDSVID RWRGKVLTKS EKGV

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Macromolecule #3: DNA (5'-D(P*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*A)-3')

MacromoleculeName: DNA (5'-D(P*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*A)-3')
type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Agrobacterium tumefaciens (bacteria)
Molecular weightTheoretical: 4.894239 KDa
SequenceString:
(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)

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Macromolecule #4: DNA (5'-D(*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*T)-3')

MacromoleculeName: DNA (5'-D(*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*T)-3')
type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Agrobacterium tumefaciens (bacteria)
Molecular weightTheoretical: 5.198432 KDa
SequenceString:
(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)

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Macromolecule #5: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 6 / 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 #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 6 / 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 63.01 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.902 µm / Nominal defocus min: 0.456 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 88914
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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