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- EMDB-49920: Structure of Hailong HalA in complex with oligodeoxyadenylate -

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Basic information

Entry
Database: EMDB / ID: EMD-49920
TitleStructure of Hailong HalA in complex with oligodeoxyadenylate
Map dataunsharpened map
Sample
  • Complex: HalA in complex with ODA
    • Protein or peptide: HalA
KeywordsHailong / ion channel / oligodeoxyadenylate / anti-phage defense / ANTIVIRAL PROTEIN
Biological speciesRhodobacteraceae bacterium QY30 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.98 Å
AuthorsTan JMJ / Melamed S / Cofsky JC / Syangtan D / Hobbs SJ / Del Marmol J / Jost M / Kruse AC / Sorek R / Kranzusch PJ
Funding support United States, 1 items
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 26, 2025-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49920.png

Downloads & links

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Map

FileDownload / File: emd_49920.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened map
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AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 384 pix.
= 282.624 Å		0.74 Å/pix.
x 384 pix.
= 282.624 Å		0.74 Å/pix.
x 384 pix.
= 282.624 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.736 Å
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Contour LevelBy AUTHOR: 0.0386
Minimum - Maximum-0.07286679 - 0.25197694
Average (Standard dev.)0.0006762307 (±0.0053372714)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 282.624 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49920_msk_1.map
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Mask #2

Fileemd_49920_msk_2.map
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Additional map: density-modified map

Fileemd_49920_additional_1.map
Annotationdensity-modified map
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Half map: half map A

Fileemd_49920_half_map_1.map
Annotationhalf map A
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Half map: half map B

Fileemd_49920_half_map_2.map
Annotationhalf map B
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Sample components

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Entire : HalA in complex with ODA

EntireName: HalA in complex with ODA
Components
  • Complex: HalA in complex with ODA
    • Protein or peptide: HalA

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Supramolecule #1: HalA in complex with ODA

SupramoleculeName: HalA in complex with ODA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rhodobacteraceae bacterium QY30 (bacteria)

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Macromolecule #1: HalA

MacromoleculeName: HalA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacteraceae bacterium QY30 (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH GSLDTNAVKE PEPALPSAAS RGRRTKNWWE PMFDANAPAS FSVSDWNFSN NRGPRCTLFL AEKMPDATTL VVKDIDFQDC DFQGTFERKI VFKDCKFTRC DFGLSTFSRT KFSGCSFYAS SFTQCTLENC EFRNCKYEKI FYSGNETQIP RTLIAEPYQF ...String:
MGSSHHHHHH GSLDTNAVKE PEPALPSAAS RGRRTKNWWE PMFDANAPAS FSVSDWNFSN NRGPRCTLFL AEKMPDATTL VVKDIDFQDC DFQGTFERKI VFKDCKFTRC DFGLSTFSRT KFSGCSFYAS SFTQCTLENC EFRNCKYEKI FYSGNETQIP RTLIAEPYQF LFGACATVDS VPQGKSRFEQ RARFEETRST IARALLANLH SEGSEDTYYA AVKASTLSEN RARIARALIK INSSASKGKS IISRAVSFLT GFASAISAVV GMLILLVMGS LNGWGSSISR AMLVGVVAIS CVAYRYHYRF NLPPEDAMVK ATEIFFLFGY TNYAKMGQED FHLVFSNALL GLFWYAIAIP TISNRLTRAR G

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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: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.038 kPa / Details: 30 s glow, 10 s hold. easiGlow (Pelco). Negative.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 10951 / Average electron dose: 53.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1247992
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: cryoSPARC ab initio
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 1.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 231898
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
FSC plot (resolution estimation)

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