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- PDB-21fy: The cryo-EM structure of IscS-PptA complex -

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Basic information

Entry
Database: PDB / ID: 21fy
TitleThe cryo-EM structure of IscS-PptA complex
Components
  • Cysteine desulfurase IscS
  • PptA
KeywordsVIRAL PROTEIN / DNA phosphorothioation / anti-defense system
Function / homology
Function and homology information


detection of UV / tRNA 4-thiouridine biosynthesis / sulfur compound transport / L-selenocysteine catabolic process / selenocysteine lyase activity / L-cysteine desulfurase complex / tRNA wobble position uridine thiolation / sulfur carrier activity / cysteine desulfurase / cysteine desulfurase activity ...detection of UV / tRNA 4-thiouridine biosynthesis / sulfur compound transport / L-selenocysteine catabolic process / selenocysteine lyase activity / L-cysteine desulfurase complex / tRNA wobble position uridine thiolation / sulfur carrier activity / cysteine desulfurase / cysteine desulfurase activity / L-cysteine catabolic process / thiamine biosynthetic process / [2Fe-2S] cluster assembly / iron-sulfur cluster assembly / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / metal ion binding / cytosol
Similarity search - Function
Cysteine desulfurase IscS / Cysteine desulfurase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Rossmann-like alpha/beta/alpha sandwich fold / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Uncharacterized protein / Cysteine desulfurase IscS
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Psychrobacter phage vB_PmaS_Y8A (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsWang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Microbiol / Year: 2026
Title: Phage hijacks host phosphorothioate DNA modification machinery to circumvent bacterial Ssp defences.
Authors: Yifei Wang / Haoyi Yang / Lixu Jiang / Yashi Ge / Yuhang Zhong / Hui Chu / Kuo Zhang / Kadierya Kuerban / Yuan Nong / Haiyan Gao / Congrui Xu / Xiaoyu Li / Shi Chen / Lianrong Wang /
Abstract: The bacterial Ssp defence system discriminates self from non-self by introducing sequence-specific phosphorothioate (PT) modifications in host DNA (via SspABCD) and cleaving unmodified foreign DNA ...The bacterial Ssp defence system discriminates self from non-self by introducing sequence-specific phosphorothioate (PT) modifications in host DNA (via SspABCD) and cleaving unmodified foreign DNA (via SspFGH or SspE). Here we report PptA, a phage-encoded [4Fe-4S] cluster-containing protein, which hijacks cognate host cysteine desulfurase IscS homologues to assemble a streamlined PT modification machinery. Integrated biochemical and structural data delineate a model for intermolecular sulfur transfer within the IscS-PptA complex. Upon infection, robust expression of PptA, not merely its presence, drives sufficient PT incorporation into the phage genome, enabling molecular mimicry of host PT patterns. By masquerading as 'self', the modified phage DNA evades recognition and cleavage by SspFGH/SspE. Notably, PptA can reprogramme the Ssp-sensitive λ phage into an immune-evasive variant. These results reveal a co-evolutionary strategy used by phages to overcome PT-based bacterial immunity and provide a foundation for engineering therapeutic phages that bypass this widespread defence system.
History
DepositionDec 11, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine desulfurase IscS
B: Cysteine desulfurase IscS
C: PptA
D: PptA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,0036
Polymers151,3004
Non-polymers7032
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 Cysteine desulfurase IscS / NifS protein homolog / ThiI transpersulfidase / TusA transpersulfidase


Mass: 45377.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: iscS, nuvC, yfhO, yzzO, b2530, JW2514 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A6B7, cysteine desulfurase
#2: Protein PptA


Mass: 30272.225 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Sequence reference for Psychrobacter phage 1 is not available at the time of biocuration. Current sequence reference is from UniProt id A0A5Q2WBY0.
Source: (gene. exp.) Psychrobacter phage vB_PmaS_Y8A (virus)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5Q2WBY0
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: IscS-PptA complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Psychrobacter phage vB_PmaS_Y8A (virus)3017068
31Escherichia coli K-12 (bacteria)83333
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
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: 2500 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 363923 / Symmetry type: POINT

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