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- PDB-21rj: a bacterial caspase -

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Basic information

Entry
Database: PDB / ID: 21rj
Titlea bacterial caspase
ComponentsPsCaspase
KeywordsCELL INVASION / a bacterial caspase
Biological speciesPseudomonas aeruginosa UCBPP-PA14 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.58 Å
AuthorsWang, W.H. / Feng, Y.
Funding support China, 1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PsCaspase
B: PsCaspase
C: PsCaspase
D: PsCaspase
E: PsCaspase
F: PsCaspase
G: PsCaspase
H: PsCaspase
I: PsCaspase
J: PsCaspase


Theoretical massNumber of molelcules
Total (without water)355,99010
Polymers355,99010
Non-polymers00
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
PsCaspase


Mass: 35599.035 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: a bacterial caspase / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7.8
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: OTHER
Electron lensMode: DIFFRACTION / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1150GATAN K3 (6k x 4k)
2150GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX2.0_5885model refinement
13cryoSPARC3D reconstruction
Image processing
IDImage recording-ID
11
22
32
CTF correction
IDEM image processing-IDType
11PHASE FLIPPING AND AMPLITUDE CORRECTION
22PHASE FLIPPING AND AMPLITUDE CORRECTION
33PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstruction
IDResolution (Å)Resolution methodNum. of particlesImage processing-IDEntry-IDSymmetry type
12.58FSC 0.143 CUT-OFF229477121RJPOINT
22.58FSC 0.143 CUT-OFF229477121RJPOINT
32.58FSC 0.143 CUT-OFF229477121RJPOINT
42.58FSC 0.143 CUT-OFF229477221RJPOINT
52.58FSC 0.143 CUT-OFF229477221RJPOINT
62.58FSC 0.143 CUT-OFF229477221RJPOINT
72.58FSC 0.143 CUT-OFF229477321RJPOINT
82.58FSC 0.143 CUT-OFF229477321RJPOINT
92.58FSC 0.143 CUT-OFF229477321RJPOINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 56.79 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004124242
ELECTRON MICROSCOPYf_angle_d0.561832896
ELECTRON MICROSCOPYf_chiral_restr0.04483648
ELECTRON MICROSCOPYf_plane_restr0.00544350
ELECTRON MICROSCOPYf_dihedral_angle_d4.50253326

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