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- PDB-9wuf: Cryo-EM structure of Upx -

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Basic information

Entry
Database: PDB / ID: 9wuf
TitleCryo-EM structure of Upx
ComponentsRestriction endonuclease
KeywordsANTIVIRAL PROTEIN / protein structure
Function / homology: / : / Anti-phage protein Upx-like / Uncharacterized protein
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Bredeney (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsZhang, H. / Li, X.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Nat Commun / Year: 2026
Title: Structural and mechanistic insights into the dual-nuclease defense protein Upx as an anti-phage system.
Authors: Ruimin Zhou / Yingcan Liu / Qian Zhang / Zhenning Yin / Jiajing Tong / Chendi Zhang / Lingling Zhang / Xuzichao Li / Yanhao Zhao / Shuqin Zhang / Zhikun Liu / Weichang Chen / Nan Ji / Heng ...Authors: Ruimin Zhou / Yingcan Liu / Qian Zhang / Zhenning Yin / Jiajing Tong / Chendi Zhang / Lingling Zhang / Xuzichao Li / Yanhao Zhao / Shuqin Zhang / Zhikun Liu / Weichang Chen / Nan Ji / Heng Zhang / Zhuang Li / Hang Yin / Shengkai Zuo / Yong Wei /
Abstract: Nucleic acid degradation is a common strategy for prokaryotic anti-phage systems, as exemplified by the CRISPR-Cas system. The PD-(D/E)-XK nucleases constitute a widely distributed family in these ...Nucleic acid degradation is a common strategy for prokaryotic anti-phage systems, as exemplified by the CRISPR-Cas system. The PD-(D/E)-XK nucleases constitute a widely distributed family in these defenses. Notably, most members exhibit a single nuclease domain, while variants containing dual nuclease domains within a single polypeptide remain underexplored, and their molecular mechanisms largely obscure. Here, we biochemically and functionally study a single-protein system containing an uncharacterized PD-(D/E)-XK defense protein (Upx). As revealed by single-particle electron cryo-microscopy (cryo-EM) structure, the C-terminal domain (CTD) harboring the conserved PD-(D/E)XK catalytic core is buttressed by the N-terminal domain (NTD) and the middle domain (MD). Functional assays demonstrate that the nucleic acid binding capability of the CTD is enhanced by the MD. The NTD also displays a noncanonical, basal exonuclease activity that is auto-inhibited by MD. IP-MS experiments identify Upx-interacting phage proteins, and substrate profiling defines its physiological preferences, collectively pointing to its potential physiological targets. Notably, the phage protein gp16 was found to relieve MD-mediated inhibition of the NTD, suggesting a virus-triggered mechanism for activating Upx's dual nuclease activity. Together, these findings establish Upx as a single-protein dual-nuclease anti-phage system, expanding our understanding of bacterial immunity and informing antiviral strategy development.
History
DepositionSep 18, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Restriction endonuclease


Theoretical massNumber of molelcules
Total (without water)143,0251
Polymers143,0251
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 Restriction endonuclease


Mass: 143024.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Bredeney (bacteria)
Gene: CB674_22005, CS511_22705, D8R59_19620, EPA75_24960 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3V9PQ34
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: protein structure / Type: CELL / Entity ID: all / Source: NATURAL
Source (natural)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

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 defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 204860 / Symmetry type: POINT

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