21FY | pdb_000021fy

The cryo-EM structure of IscS-PptA complex

• PDB DOI: https://doi.org/10.2210/pdb21FY/pdb
• EM Map EMD-67634: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Escherichia coli K-12, Psychrobacter phage vB_PmaS_Y8A
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-12-11 Released: 2026-04-15 
• Deposition Author(s): Wang, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.85 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Phage hijacks host phosphorothioate DNA modification machinery to circumvent bacterial Ssp defences.

Wang, Y., Yang, H., Jiang, L., Ge, Y., Zhong, Y., Chu, H., Zhang, K., Kuerban, K., Nong, Y., Gao, H., Xu, C., Li, X., Chen, S., Wang, L.

(2026) Nat Microbiol 11: 2187-2200

• PubMed: 42527632 
• DOI: https://doi.org/10.1038/s41564-026-02387-3
• Primary Citation Related Structures: 
  21FY


• PubMed 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 (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.

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Organizational Affiliation: 
• Department of Gastroenterology, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.
Department of Respiratory Diseases, Institute of Pediatrics, Shenzhen Children's Hospital ＆ Shenzhen University Medical School, Shenzhen, China.
Department of Critical Care Medicine, Intensive Care Unit, Shenzhen Key Laboratory of Microbiology in Genomic Modification and Editing and Application, Shenzhen Institute of Translational Medicine, Shenzhen University Medical School, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.
School of Bioengineering, Dalian University of Technology, Dalian, China.
Department of Gastroenterology, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China. [e-mail].
Department of Critical Care Medicine, Intensive Care Unit, Shenzhen Key Laboratory of Microbiology in Genomic Modification and Editing and Application, Shenzhen Institute of Translational Medicine, Shenzhen University Medical School, The First Affiliated Hospital of Shenzhen University, Shenzhen, China. [e-mail].
Department of Respiratory Diseases, Institute of Pediatrics, Shenzhen Children's Hospital ＆ Shenzhen University Medical School, Shenzhen, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 152 kDa 
• Atom Count: 9,912 
• Modeled Residue Count: 1,258 
• Deposited Residue Count: 1,348 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine desulfurase IscS	A, B	404	Escherichia coli K-12	Mutation(s): 0  Gene Names: iscS, nuvC, yfhO, yzzO, b2530, JW2514 EC: 2.8.1.7
UniProt
Find proteins for P0A6B7 (Escherichia coli (strain K12)) Explore P0A6B7  Go to UniProtKB:  P0A6B7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PptA	C, D	270	Psychrobacter phage vB_PmaS_Y8A	Mutation(s): 0
UniProt
Find proteins for A0A5Q2WBY0 (Vibrio phage vB_VhaP_VH-5) Explore A0A5Q2WBY0  Go to UniProtKB:  A0A5Q2WBY0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4 (Subject of Investigation/LOI)	E [auth C], F [auth D]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.85 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-04-15 
Deposition Author(s): Wang, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2026-04-15
  Type: Initial release
  
• Version 1.1: 2026-08-12
  Type: Remediation
  Reason: Metalloprotein remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2026-08-19
  Changes: Data collection, Database references