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- EMDB-67942: a bacterial caspase bound to ligand -

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Basic information

Entry
Database: EMDB / ID: EMD-67942
Titlea bacterial caspase bound to ligand
Map data
Sample
  • Complex: a bacterial caspase bound to ligand
    • Protein or peptide: PsCaspase
  • Ligand: Adenosine 5'-diphosphate-cyclo[N7:1'']-ribose
Keywordsa bacterial caspase bound to ligand / CELL INVASION
Biological speciesPseudomonas aeruginosa UCBPP-PA14 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsWang WH / Feng Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32030056 China
CitationJournal: Vita / Year: 2026
Title: Caspase forms double-stranded helical assembly during the type IV Thoeris
Authors: Wei L / Shu X / Wang W / Li F / Fan Y / Li D / Wang R / Liu J / Wang Q / Jiang L / He L / Duan S / Zhao L / Zhang S / Ren J / Zhang Y / Li M / Feng Y
History
DepositionDec 23, 2025-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67942.png

Downloads & links

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Map

FileDownload / File: emd_67942.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 600 pix.
= 396. Å		0.66 Å/pix.
x 600 pix.
= 396. Å		0.66 Å/pix.
x 600 pix.
= 396. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.5521641 - 0.8941012
Average (Standard dev.)0.0004374442 (±0.027008189)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 396.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_67942_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_67942_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_67942_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 : a bacterial caspase bound to ligand

EntireName: a bacterial caspase bound to ligand
Components
  • Complex: a bacterial caspase bound to ligand
    • Protein or peptide: PsCaspase
  • Ligand: Adenosine 5'-diphosphate-cyclo[N7:1'']-ribose

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Supramolecule #1: a bacterial caspase bound to ligand

SupramoleculeName: a bacterial caspase bound to ligand / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pseudomonas aeruginosa UCBPP-PA14 (bacteria)

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Macromolecule #1: PsCaspase

MacromoleculeName: PsCaspase / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Molecular weightTheoretical: 35.599035 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MRKALVVGID HYASVSALYG CVNDSFAVKA MLDRHADGSV NFGVKHLTAT GPSDSVPRDE FRQAIEELFS GDGEISLLYF AGHGHIEAT GGYLCSSDVK TGHDGVSLAE IMTMANQSRV QNRVVILDSC HSGVAGGRAL QQHVAEISDG VTILTASTAE Q YATEENGA ...String:
MRKALVVGID HYASVSALYG CVNDSFAVKA MLDRHADGSV NFGVKHLTAT GPSDSVPRDE FRQAIEELFS GDGEISLLYF AGHGHIEAT GGYLCSSDVK TGHDGVSLAE IMTMANQSRV QNRVVILDSC HSGVAGGRAL QQHVAEISDG VTILTASTAE Q YATEENGA GVFTSLLVDA LGGAAANLVG DVTPGGVYAH VDQSLGPWAQ RPVFKTNVKR FVSLRKVQPP LELAELRRIS EF FPNPGFQ FQLDPSYEPE RHKSWENNPE GIPAPNPDHN AVFKILQKYN RVGLVVPEGA PHMWHAAMES KFIRLTALGE HYR QLAEKG LI

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Macromolecule #2: Adenosine 5'-diphosphate-cyclo[N7:1'']-ribose

MacromoleculeName: Adenosine 5'-diphosphate-cyclo[N7:1'']-ribose / type: ligand / ID: 2 / Number of copies: 8 / Formula: A1EZF
Molecular weightTheoretical: 543.316 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.8
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: OTHER / Imaging mode: DIFFRACTION / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 112822
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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