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- PDB-9ykj: Hna Dimer -

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Basic information

Entry
Database: PDB / ID: 9ykj
TitleHna Dimer
ComponentsHelicase ATP-binding domain-containing protein
KeywordsIMMUNE SYSTEM / PD(D/E)XK nuclease / Superfamily 2 helicase / Anti-bacteriophage protein
Function / homology
Function and homology information


hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / nucleobase-containing compound metabolic process / helicase activity / DNA binding / ATP binding
Similarity search - Function
HELICc2 / ATP-dependent helicase, C-terminal / Helicase C-terminal domain / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Helicase ATP-binding domain-containing protein
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsHooper, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Welch FoundationF-1938 United States
CitationJournal: bioRxiv / Year: 2025
Title: Phage-encoded factor stimulates DNA degradation by the Hna anti-phage defense system.
Authors: Matthew M Hooper / Benjamin T Hoover / Hongshan Zhang / Adam S Franco / Ilya J Finkelstein / David W Taylor
Abstract: Prokaryotic organisms have evolved unique strategies to acquire immunity against the constant threat of bacteriophage (phage) and mobile genetic elements. Hna is a broadly distributed anti-phage ...Prokaryotic organisms have evolved unique strategies to acquire immunity against the constant threat of bacteriophage (phage) and mobile genetic elements. Hna is a broadly distributed anti-phage immune system that confers resistance against diverse phage by eliciting an abortive infection response. Using a combination of biochemistry, cryo-electron microscopy, and single-molecule fluorescence imaging, we reveal that Hna functions as a 3'-5' single-stranded DNA exonuclease that forms an auto-inhibited dimer under physiological ATP concentrations. We observed that Hna autoinhibition can be overcome by incorporation of a phage-encoded single-stranded DNA binding protein (SSB), stimulating unregulated Hna nuclease activity. Furthermore, phage escape mutants encode SSB variants that evade Hna surveillance by adopting higher order stoichiometries with enhanced DNA binding affinity. Our work establishes the molecular basis of Hna-mediated anti-phage activity and provides novel insights into how phage-encoded proteins can directly stimulate a bacterial immune response.
History
DepositionOct 7, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Helicase ATP-binding domain-containing protein
B: Helicase ATP-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,5374
Polymers189,6832
Non-polymers8542
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 Helicase ATP-binding domain-containing protein


Mass: 94841.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Gene: SMa2245 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92XN4
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY
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: Hna Dimer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: .1894 MDa / Experimental value: NO
Source (natural)Organism: Sinorhizobium meliloti (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 49 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21_5207model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 183538 / Symmetry type: POINT
RefinementHighest resolution: 3.44 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0089727
ELECTRON MICROSCOPYf_angle_d1.45913159
ELECTRON MICROSCOPYf_dihedral_angle_d12.041347
ELECTRON MICROSCOPYf_chiral_restr0.0821466
ELECTRON MICROSCOPYf_plane_restr0.0111692

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