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- EMDB-71389: Structure of CloA in complex with dGTP and p3diT -

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Basic information

Entry
Database: EMDB / ID: EMD-71389
TitleStructure of CloA in complex with dGTP and p3diT
Map data
Sample
  • Complex: Octameric complex of CloA in complex with dGTP and p3diT
    • Protein or peptide: DNTP triphosphohydrolase
    • DNA: 5'-triphosphothymidyl-3'5'-thymidine (p3diT)
  • Ligand: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsdeoxynucleoside triphosphohydrolase / HYDROLASE
Function / homology
Function and homology information


dGTPase activity / dGTP catabolic process
Similarity search - Function
Deoxyguanosinetriphosphate triphosphohydrolase, C-terminal / Deoxyguanosinetriphosphate triphosphohydrolase, central domain superfamily / dNTP triphosphohydrolase / : / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain
Similarity search - Domain/homology
DNTP triphosphohydrolase
Similarity search - Component
Biological speciesSalmonella enterica (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.56 Å
AuthorsYamaguchi S / Fernandez SG / Wassarman DR / Luder M / Schwede F / Kranzusch PJ
Funding support Japan, France, United States, 3 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)202360072 Japan
Human Frontier Science Program (HFSP)LT0051 France
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2 GM146250-01 United States
CitationJournal: bioRxiv / Year: 2025
Title: Activating and inhibiting nucleotide signals coordinate bacterial anti-phage defense.
Authors: Sonomi Yamaguchi / Samantha G Fernandez / Douglas R Wassarman / Marlen Lüders / Frank Schwede / Philip J Kranzusch /
Abstract: The cellular nucleotide pool is a major focal point of the host immune response to viral infection. Immune effector proteins that disrupt the nucleotide pool allow animal and bacterial cells to ...The cellular nucleotide pool is a major focal point of the host immune response to viral infection. Immune effector proteins that disrupt the nucleotide pool allow animal and bacterial cells to broadly restrict diverse viruses, but reduced nucleotide availability induces cellular toxicity and can limit host fitness(Ahmad et al., 1998; Goldstone et al., 2011; Hsueh et al., 2022; Itsko & Schaaper, 2014; Tal et al., 2022). Here we discover a bacterial anti-phage defense system named Clover that overcomes this tradeoff by encoding a deoxynucleoside triphosphohydrolase enzyme (CloA) that dynamically responds to both an activating phage cue and an inhibitory nucleotide immune signal produced by a partnering regulatory enzyme (CloB). Analysis of Clover phage restriction in cells and reconstitution of enzymatic function in vitro demonstrate that CloA is a dGTPase that responds to viral enzymes that increase cellular levels of dTTP. To restrain CloA activation in the absence of infection, we show that CloB synthesizes a dTTP-related inhibitory nucleotide signal p3diT (5'-triphosphothymidyl-3'5'-thymidine) that binds to CloA and suppresses activation. Cryo-EM structures of CloA in activated and suppressed states reveal how dTTP and p3diT control distinct allosteric sites and regulate effector function. Our results define how nucleotide signals coordinate both activation and inhibition of antiviral immunity and explain how cells balance defense and immune-mediated toxicity.
History
DepositionJun 23, 2025-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71389.png

Downloads & links

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Map

FileDownload / File: emd_71389.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.266
Minimum - Maximum-0.22867608 - 0.877878
Average (Standard dev.)-0.00035852866 (±0.02029847)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_71389_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71389_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 : Octameric complex of CloA in complex with dGTP and p3diT

EntireName: Octameric complex of CloA in complex with dGTP and p3diT
Components
  • Complex: Octameric complex of CloA in complex with dGTP and p3diT
    • Protein or peptide: DNTP triphosphohydrolase
    • DNA: 5'-triphosphothymidyl-3'5'-thymidine (p3diT)
  • Ligand: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Octameric complex of CloA in complex with dGTP and p3diT

SupramoleculeName: Octameric complex of CloA in complex with dGTP and p3diT
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Salmonella enterica (bacteria)

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Macromolecule #1: DNTP triphosphohydrolase

MacromoleculeName: DNTP triphosphohydrolase / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica (bacteria)
Molecular weightTheoretical: 54.257172 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GSMHWNDLLN SNRRKPKNEK KESSQDTSKG RQQIERDYDR ILFAAPTRRL ADKTQVFPLD KNDSVRTRLT HSHEVANLSR GIGMRLAFE LEDDVFKDVS EDICLKRDVP ALLAAIGLVH DMGNPPFGAQ GAKAMSEWFT KNLPEHSDNY KDKIYGDFRH F DGNSQTLR ...String:
GSMHWNDLLN SNRRKPKNEK KESSQDTSKG RQQIERDYDR ILFAAPTRRL ADKTQVFPLD KNDSVRTRLT HSHEVANLSR GIGMRLAFE LEDDVFKDVS EDICLKRDVP ALLAAIGLVH DMGNPPFGAQ GAKAMSEWFT KNLPEHSDNY KDKIYGDFRH F DGNSQTLR LVTKLQILND TYGLNLTYAT LASMIKYPRS SESDSSLWKK HGFFLSEKDV VQDIWNNTGL SEGVRHPFTY IM EACDDIA YSVLDAEDII KKGFASFHDL IDFIQSNQFC KEDDVAKRVI ENCKKIHADY AQQKLSPAEL NDMSMQMFRV YAI AELVDA VVIAFKDNIN EFLNDTCEIK DLISCSSGKN LCQALKKFDS SRGYQHRSVL KLELEGSNYI KGLMDMLWLG IKGR ATGDT QYDTPFGRYV YGRISENYRR IFEQENNLPA CYKEAQLLAD AISGMTDSYL IALHDELRAL HQYECRQR

UniProtKB: DNTP triphosphohydrolase

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Macromolecule #2: 5'-triphosphothymidyl-3'5'-thymidine (p3diT)

MacromoleculeName: 5'-triphosphothymidyl-3'5'-thymidine (p3diT) / type: dna / ID: 2 / Number of copies: 8 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 723.388 Da
SequenceString:
(TTP)(DT)

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Macromolecule #3: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 8 / Formula: DGT
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-DGT:
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 8 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.24 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Alphafold3 model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1498407
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: MAXIMUM LIKELIHOOD

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