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- PDB-8zue: cryo-electron microscopy (cryo-EM) structure of the Hachiman defe... -

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Basic information

Entry
Database: PDB / ID: 8zue
Titlecryo-electron microscopy (cryo-EM) structure of the Hachiman defense system from Escherichia coli
Components
  • Anti-bacteriophage protein A
  • Anti-bacteriophage protein B
KeywordsDNA BINDING PROTEIN / Bacterial Hachiman complex / DNA cleavage / antiphage defense
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsCui, Y.Q. / Dai, Z.K. / Ouyang, Y.F. / Wang, Y.J. / Guan, Z.Y. / Zou, T.T.
Funding support China, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anti-bacteriophage protein A
B: Anti-bacteriophage protein B


Theoretical massNumber of molelcules
Total (without water)148,1942
Polymers148,1942
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Anti-bacteriophage protein A


Mass: 65024.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: abpA, yfjL, b2628, JW2609 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52127
#2: Protein Anti-bacteriophage protein B / Probable helicase AbpB


Mass: 83169.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: abpB, yfjK, b2627, JW2608 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52126
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: HamA-HamB complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
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: 1500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 440333 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039728
ELECTRON MICROSCOPYf_angle_d0.51813158
ELECTRON MICROSCOPYf_dihedral_angle_d4.2251291
ELECTRON MICROSCOPYf_chiral_restr0.0411487
ELECTRON MICROSCOPYf_plane_restr0.0041690

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