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- EMDB-60482: cryo-electron microscopy (cryo-EM) structure of the Hachiman defe... -

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Basic information

Entry
Database: EMDB / ID: EMD-60482
Titlecryo-electron microscopy (cryo-EM) structure of the Hachiman defense system from Escherichia coli
Map data
Sample
  • Complex: HamA-HamB complex
    • Protein or peptide: Anti-bacteriophage protein A
    • Protein or peptide: Anti-bacteriophage protein B
KeywordsBacterial Hachiman complex / DNA cleavage / antiphage defense / DNA BINDING PROTEIN
Function / homology
Function and homology information


nuclease activity / response to ionizing radiation / helicase activity / defense response to virus / nucleic acid binding / hydrolase activity / ATP binding
Similarity search - Function
Anti-bacteriophage protein A/HamA, C-terminal domain / CD-NTase associated protein 4, DNA endonuclease domain / HamA / Cap4, dsDNA endonuclease domain / : / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. ...Anti-bacteriophage protein A/HamA, C-terminal domain / CD-NTase associated protein 4, DNA endonuclease domain / HamA / Cap4, dsDNA endonuclease domain / : / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Anti-bacteriophage protein B / Anti-bacteriophage protein A
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsCui YQ / Dai ZK / Ouyang YF / Wang YJ / Guan ZY / Zou TT
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2025
Title: Bacterial Hachiman complex executes DNA cleavage for antiphage defense.
Authors: Yongqing Cui / Zhikang Dai / Yufei Ouyang / Chunyang Fu / Yanjing Wang / Xueting Chen / Kaiyue Yang / Shuyue Zheng / Wenwen Wang / Pan Tao / Zeyuan Guan / Tingting Zou /
Abstract: Bacteria have developed a variety of immune systems to combat phage infections. The Hachiman system is a novel prokaryotic antiphage defense system comprising HamA and HamB proteins, which contains ...Bacteria have developed a variety of immune systems to combat phage infections. The Hachiman system is a novel prokaryotic antiphage defense system comprising HamA and HamB proteins, which contains the DUF1837 and helicase domains, respectively. However, the defense mechanism remains only partially understood. Here, we present the cryo-electron microscopy (cryo-EM) structure of the Hachiman defense system featuring a fusion of Cap4 nuclease domain within HamA. Further structure analysis indicates that the DUF1837 domain on HamA resembles the PD-(D/E)XK nuclease but lacks active sites. Bioinformatics analysis reveals that catalytically inactive DUF1837 domains often recruit other functional domains to fulfill anti-phage defense. HamA interacts with HamB to form a heterodimer HamAB to mediate ATP hydrolysis and execute DNA cleavage, thus implementing antiphage defense. Our findings elucidate the structural basis of the Hachiman defense complex, highlighting the critical roles of the helicase and nuclease in prokaryotic immunity.
History
DepositionJun 8, 2024-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60482.png

Downloads & links

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Map

FileDownload / File: emd_60482.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 240 pix.
= 256.8 Å		1.07 Å/pix.
x 240 pix.
= 256.8 Å		1.07 Å/pix.
x 240 pix.
= 256.8 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-3.0960264 - 4.8547797
Average (Standard dev.)-0.0012116128 (±0.09693849)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 256.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60482_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60482_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HamA-HamB complex

EntireName: HamA-HamB complex
Components
  • Complex: HamA-HamB complex
    • Protein or peptide: Anti-bacteriophage protein A
    • Protein or peptide: Anti-bacteriophage protein B

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Supramolecule #1: HamA-HamB complex

SupramoleculeName: HamA-HamB complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Macromolecule #1: Anti-bacteriophage protein A

MacromoleculeName: Anti-bacteriophage protein A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 65.024559 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH SDEVDAHMES NDSGGVAAKH GFLFQDCVAA YHVTRMLRDK TIRSVRCEVT DDIDIVSDGY IDFVQVKST GKTRWNISDI VQNSKGADKK TIPCSSILHK SMQCESDLSL GRRYSIVTEE KVNKTLEYLT ISPNARLDKP G RQELIDDL ...String:
MGSSHHHHHH SSGLVPRGSH SDEVDAHMES NDSGGVAAKH GFLFQDCVAA YHVTRMLRDK TIRSVRCEVT DDIDIVSDGY IDFVQVKST GKTRWNISDI VQNSKGADKK TIPCSSILHK SMQCESDLSL GRRYSIVTEE KVNKTLEYLT ISPNARLDKP G RQELIDDL NKRTDNFLTD SGISVSDWID AATWEVFSSL RELELLGIKN IRLASQDLHG VILSSETVAE DIWCRILDTV TR KGEHSRR IHSADDKSYL RPDLLEWFKQ RVEDDQSRSG RKIYVKRDLP HILTPFRAPM ASVCAKRKGQ VLHQQYSLKK YRY KHIADN VCQWLDEVFL RPKEMSDIHK LTFIEKRERL KNSVFKSLHD VSEFLGRVLL HATIRQHHES QPIPCMLYVE KAGA EKILE NVHIVRRDPE GDQLWIGFSE LVTDINIAVR LPEIRDQLYE DISDCIDTAR KKILDIKDDN YLLRHDIDEI LDGSQ PFDA HLDRFTFVLF VGYDSNLLTE PETPGFEDDL EKETAVLFEK FAADLIEDSP FANLCIHVFI YPAPSLERLT QLVDEK VRE VV

UniProtKB: Anti-bacteriophage protein A

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Macromolecule #2: Anti-bacteriophage protein B

MacromoleculeName: Anti-bacteriophage protein B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 83.169664 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTEIYEQAKH SLQGEDFSSF NYLFAVNKLL SNPVSYDLGR DLIVRALDSR ERFSEHTTIL KNMVRKSGLF PYLKKEFTSL TPDDLRVLE LYRTPFSDGY VFHSMQFHIF DLLKSGQNVV LSAPTSMGKS AIVDSLLGMG TLKRLVLVVP TVALADETRR R LQERFGDR ...String:
MTEIYEQAKH SLQGEDFSSF NYLFAVNKLL SNPVSYDLGR DLIVRALDSR ERFSEHTTIL KNMVRKSGLF PYLKKEFTSL TPDDLRVLE LYRTPFSDGY VFHSMQFHIF DLLKSGQNVV LSAPTSMGKS AIVDSLLGMG TLKRLVLVVP TVALADETRR R LQERFGDR YQIIHHSSQV CHSDQAVYVL TQERVNERDD IVDIDLFVID EFYKLAFRQL KSGDIDHQDE RVIELNIALS KL LKVSRQF YLTGPFVNSI RGLEKLGYPH TFVSTDFNTV ALDVKTFGIK ANDDKAKLKA LGEIAHACVD ATIIYCKSPT VAG LVAREL IRLGHGTPTE NPHVDWVSEE FDADWDYTVA LRNGIGLHFG ALPRALQQYT ADQFNAGKLR FLLCTSTIIE GVNT IAKNV VIYDNRDGTR SIDKFTHGNI KGRAGRMGVH FVGKIFCLEE IPEDNLNQEV DIPLGIQGID TPINLLASVQ PDHLS EFSQ DRFDEVFIND RVSIDLVKKH SYFRVEQFEM LQSMFEMMDD NEFSSLVFHW TPATNFLKTF AKIIARLVPH TFSRNG VPV KPTDVMIAKL AGYLSAESYS EYLKNQIDYA RQWISEGEKR TLSIALNNDL KLITNTFGYT LPKVLSLMED VVKHHAV KR GIRSKVDYTH VKLAFESFHL PPGVNALEEI GIPIQTLHRL VDLLEFSDEA DVDELSQYLR DTQDIWSRSI GYVDQMFI R RALGIRRH

UniProtKB: Anti-bacteriophage protein B

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: 1.5 µm / Nominal defocus min: 1.0 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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 440333
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD

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