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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


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
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: To Be Published
Title: The cryo-EM structure of IscS-PptA complex
Authors: Wang Y
History
DepositionDec 11, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 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

Slices (1/3)

Slices (1/2)

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

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_67634_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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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