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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


IscS-TusA complex / IscS-IscU complex / tRNA 4-thiouridine biosynthesis / sulfur compound transport / L-selenocysteine catabolic process / sulfurtransferase complex / detection of UV / selenocysteine lyase activity / L-cysteine desulfurase complex / tRNA wobble position uridine thiolation ...IscS-TusA complex / IscS-IscU complex / tRNA 4-thiouridine biosynthesis / sulfur compound transport / L-selenocysteine catabolic process / sulfurtransferase complex / detection of UV / selenocysteine lyase activity / L-cysteine desulfurase complex / tRNA wobble position uridine thiolation / sulfur carrier activity / L-cysteine catabolic process / cysteine desulfurase / cysteine desulfurase activity / 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: To Be Published
Title: The cryo-EM structure of IscS-PptA complex
Authors: Wang, Y.
History
DepositionDec 11, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Primary map / Data content type: Primary map / Provider: 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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