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- EMDB-67634: The cryo-EM structure of IscS-PptA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-67634
TitleThe cryo-EM structure of IscS-PptA complex
Map data
Sample
  • Complex: IscS-PptA complex
    • Protein or peptide: Cysteine desulfurase IscS
    • Protein or peptide: PptA
  • Ligand: IRON/SULFUR CLUSTER
KeywordsDNA phosphorothioation / anti-defense system / VIRAL PROTEIN
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
Uncharacterized protein / Cysteine desulfurase IscS
Similarity search - Component
Biological speciesPsychrobacter phage vB_PmaS_Y8A (virus) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsWang Y
Funding support China, 1 items
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, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67634.png

Downloads & links

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Map

FileDownload / File: emd_67634.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 224 pix.
= 188.16 Å		0.84 Å/pix.
x 224 pix.
= 188.16 Å		0.84 Å/pix.
x 224 pix.
= 188.16 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.018543929 - 1.9165422
Average (Standard dev.)0.0034392807 (±0.0431981)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 188.15999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_67634_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_67634_half_map_2.map
Projections & Slices
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Sample components

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Entire : IscS-PptA complex

EntireName: IscS-PptA complex
Components
  • Complex: IscS-PptA complex
    • Protein or peptide: Cysteine desulfurase IscS
    • Protein or peptide: PptA
  • Ligand: IRON/SULFUR CLUSTER

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Supramolecule #1: IscS-PptA complex

SupramoleculeName: IscS-PptA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Psychrobacter phage vB_PmaS_Y8A (virus)

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Macromolecule #1: Cysteine desulfurase IscS

MacromoleculeName: Cysteine desulfurase IscS / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: cysteine desulfurase
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 45.377594 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKLPIYLDYS ATTPVDPRVA EKMMQFMTMD GTFGNPASRS HRFGWQAEEA VDIARNQIAD LVGADPREIV FTSGATESDN LAIKGAANF YQKKGKHIIT SKTEHKAVLD TCRQLEREGF EVTYLAPQRN GIIDLKELEA AMRDDTILVS IMHVNNEIGV V QDIAAIGE ...String:
MKLPIYLDYS ATTPVDPRVA EKMMQFMTMD GTFGNPASRS HRFGWQAEEA VDIARNQIAD LVGADPREIV FTSGATESDN LAIKGAANF YQKKGKHIIT SKTEHKAVLD TCRQLEREGF EVTYLAPQRN GIIDLKELEA AMRDDTILVS IMHVNNEIGV V QDIAAIGE MCRARGIIYH VDATQSVGKL PIDLSQLKVD LMSFSGH(LLP)IY GPKGIGALYV RRKPRVRIEA QMHGGGHE R GMRSGTLPVH QIVGMGEAYR IAKEEMATEM ERLRGLRNRL WNGIKDIEEV YLNGDLEHGA PNILNVSFNY VEGESLIMA LKDLAVSSGS ACTSASLEPS YVLRALGLND ELAHSSIRFS LGRFTTEEEI DYTIELVRKS IGRLRDLSPL WEMYKQGVDL NSIEWAHH

UniProtKB: Cysteine desulfurase IscS

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Macromolecule #2: PptA

MacromoleculeName: PptA / type: protein_or_peptide / ID: 2
Details: Sequence reference for Psychrobacter phage 1 is not available at the time of biocuration. Current sequence reference is from UniProt id A0A5Q2WBY0.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Psychrobacter phage vB_PmaS_Y8A (virus)
Molecular weightTheoretical: 30.272225 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MSTNSPRVLC HFSCGAPSAV ATKLAIEKYG KDNVTVFNIQ ITEEHPDNQR FLKECELWFG VPVTTVRNE NFKGSIYEVF KQGFIKSPQG AACTTQLKRK VRASFQNPDD IHVFGFTTEE EQRAIDFNER NPSLTTDWVL L DAGFNRND ...String:
MGSSHHHHHH SSGLVPRGSH MSTNSPRVLC HFSCGAPSAV ATKLAIEKYG KDNVTVFNIQ ITEEHPDNQR FLKECELWFG VPVTTVRNE NFKGSIYEVF KQGFIKSPQG AACTTQLKRK VRASFQNPDD IHVFGFTTEE EQRAIDFNER NPSLTTDWVL L DAGFNRND CLGVLAGVGI GIPQMYKLGY NNNNCVGCVK GGMGYWNKIR KDFPHVFARM AMVEREVGHS LLKDKDGAVW LD ELDPDRG RMSKEPDIEC SLVCSSTLET LNN

UniProtKB: Uncharacterized protein

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Macromolecule #3: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 363923
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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