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- PDB-9nyi: Structure of HalA in complex with oligodeoxyadenylate -

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Basic information

Entry
Database: PDB / ID: 9nyi
TitleStructure of HalA in complex with oligodeoxyadenylate
Components
  • DNA (5'-D(*AP*AP*AP*AP*AP*A)-3')
  • Structure of HalA in complex with oligodeoxyadenylate
KeywordsANTIVIRAL PROTEIN / Hailong / ion channel / oligodeoxyadenylate / anti-phage defense
Function / homologyDNA
Function and homology information
Biological speciesRhodobacteraceae bacterium QY30 (bacteria)
DNA molecule (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.98 Å
AuthorsTan, J.M.J. / Melamed, S. / Cofsky, J.C. / Syangtan, D. / Hobbs, S.J. / Del Marmol, J. / Jost, M. / Kruse, A.C. / Sorek, S. / Kranzusch, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM146250 United States
CitationJournal: Nature / Year: 2025
Title: A DNA-gated molecular guard controls bacterial Hailong anti-phage defence.
Authors: Joel M J Tan / Sarah Melamed / Joshua C Cofsky / Deepsing Syangtan / Samuel J Hobbs / Josefina Del Mármol / Marco Jost / Andrew C Kruse / Rotem Sorek / Philip J Kranzusch /
Abstract: Animal and bacterial cells use nucleotidyltransferase (NTase) enzymes to respond to viral infection and control major forms of immune signalling including cGAS-STING innate immunity and CBASS anti- ...Animal and bacterial cells use nucleotidyltransferase (NTase) enzymes to respond to viral infection and control major forms of immune signalling including cGAS-STING innate immunity and CBASS anti-phage defence. Here we discover a family of bacterial defence systems, which we name Hailong, that use NTase enzymes to constitutively synthesize DNA signals and guard against phage infection. Hailong protein B (HalB) is an NTase that converts deoxy-ATP into single-stranded DNA oligomers. A series of X-ray crystal structures define a stepwise mechanism of HalB DNA synthesis initiated by a C-terminal tyrosine residue that enables de novo enzymatic priming. We show that HalB DNA signals bind to and repress activation of a partnering Hailong protein A (HalA) effector complex. A 2.0-Å cryo-electron microscopy structure of the HalA-DNA complex reveals a membrane protein with a conserved ion channel domain and a unique crown domain that binds the DNA signal and gates activation. Analysing Hailong defence in vivo, we demonstrate that viral DNA exonucleases required for phage replication trigger release of the primed HalA complex and induce protective host cell growth arrest. Our results explain how inhibitory nucleotide immune signals can serve as molecular guards against phage infection and expand the mechanisms NTase enzymes use to control antiviral immunity.
History
DepositionMar 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Structure of HalA in complex with oligodeoxyadenylate
B: Structure of HalA in complex with oligodeoxyadenylate
C: Structure of HalA in complex with oligodeoxyadenylate
D: Structure of HalA in complex with oligodeoxyadenylate
E: DNA (5'-D(*AP*AP*AP*AP*AP*A)-3')
F: DNA (5'-D(*AP*AP*AP*AP*AP*A)-3')
G: DNA (5'-D(*AP*AP*AP*AP*AP*A)-3')
H: DNA (5'-D(*AP*AP*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)173,3268
Polymers173,3268
Non-polymers00
Water11,962664
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
Structure of HalA in complex with oligodeoxyadenylate


Mass: 41497.109 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacteraceae bacterium QY30 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)
#2: DNA chain
DNA (5'-D(*AP*AP*AP*AP*AP*A)-3')


Mass: 1834.283 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 664 / Source method: isolated from a natural source / Formula: H2O
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: Structure of Hailong HalA in complex with oligodeoxyadenylate
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Rhodobacteraceae bacterium QY30 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 30 s glow, 10 s hold. easiGlow (Pelco). Negative. / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 53.8 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10951
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategoryDetails
1Topaz0.2.5particle selection
2cryoSPARC4.4.1particle selectionTopaz was run within cryoSPARC
3EPU3.6image acquisition
5cryoSPARC4.4.1CTF correction
10cryoSPARC4.4.1initial Euler assignment
11cryoSPARC4.4.1final Euler assignment
12cryoSPARC4.4.1classification
13cryoSPARC4.4.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1247992
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 1.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 231898 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model

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