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- PDB-21rh: a bacterial caspase bound to ligand -

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Basic information

Entry
Database: PDB / ID: 21rh
Titlea bacterial caspase bound to ligand
ComponentsPsCaspase
KeywordsCELL INVASION / a bacterial caspase bound to ligand
Function / homology:
Function and homology information
Biological speciesPseudomonas aeruginosa UCBPP-PA14 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 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
K: PsCaspase
L: PsCaspase
M: PsCaspase
N: PsCaspase
O: PsCaspase
P: PsCaspase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)573,93124
Polymers569,58516
Non-polymers4,3478
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.: 16
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)
#2: Chemical
ChemComp-A1EZF / Adenosine 5'-diphosphate-cyclo[N7:1'']-ribose / N7-cADPR


Mass: 543.316 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C15H23N5O13P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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 bound to ligand / Type: COMPLEX / Entity ID: #1 / 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 recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX2.0_5885model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 112822 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 63.62 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002236320
ELECTRON MICROSCOPYf_angle_d0.476949286
ELECTRON MICROSCOPYf_chiral_restr0.04265520
ELECTRON MICROSCOPYf_plane_restr0.00416422
ELECTRON MICROSCOPYf_dihedral_angle_d4.72014938

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