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- PDB-22kg: Cryo-EM Structure of a 24mer MucD cage -

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Basic information

Entry
Database: PDB / ID: 22kg
TitleCryo-EM Structure of a 24mer MucD cage
ComponentsProbable periplasmic serine endoprotease DegP-like
KeywordsHYDROLASE / Protease / Cryo-EM
Function / homology
Function and homology information


peptidase Do / periplasmic space / serine-type endopeptidase activity / signal transduction / proteolysis
Similarity search - Function
Peptidase S1C, Do / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Peptidase S1, PA clan
Similarity search - Domain/homology
Probable periplasmic serine endoprotease DegP-like
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsJiang, Y.J. / Gao, Y.G.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: To Be Published
Title: Cryo-EM Structure of a 24mer MucD cage bound to the client peptide AlgK_369-388
Authors: Jiang, Y.J. / Gao, Y.G.
History
DepositionJan 14, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 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: Probable periplasmic serine endoprotease DegP-like
B: Probable periplasmic serine endoprotease DegP-like
E: Probable periplasmic serine endoprotease DegP-like
G: Probable periplasmic serine endoprotease DegP-like
H: Probable periplasmic serine endoprotease DegP-like
K: Probable periplasmic serine endoprotease DegP-like
M: Probable periplasmic serine endoprotease DegP-like
N: Probable periplasmic serine endoprotease DegP-like
Q: Probable periplasmic serine endoprotease DegP-like
S: Probable periplasmic serine endoprotease DegP-like
T: Probable periplasmic serine endoprotease DegP-like
W: Probable periplasmic serine endoprotease DegP-like
Y: Probable periplasmic serine endoprotease DegP-like
Z: Probable periplasmic serine endoprotease DegP-like
c: Probable periplasmic serine endoprotease DegP-like
e: Probable periplasmic serine endoprotease DegP-like
f: Probable periplasmic serine endoprotease DegP-like
i: Probable periplasmic serine endoprotease DegP-like
k: Probable periplasmic serine endoprotease DegP-like
l: Probable periplasmic serine endoprotease DegP-like
o: Probable periplasmic serine endoprotease DegP-like
q: Probable periplasmic serine endoprotease DegP-like
r: Probable periplasmic serine endoprotease DegP-like
u: Probable periplasmic serine endoprotease DegP-like


Theoretical massNumber of molelcules
Total (without water)1,228,61924
Polymers1,228,61924
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 ...
Probable periplasmic serine endoprotease DegP-like / Protease Do


Mass: 51192.441 Da / Num. of mol.: 24 / Fragment: PDZ1 / Mutation: S217A
Source method: isolated from a genetically manipulated source
Details: All chains contain the S217A mutation and a 6*His tag at C-ter. Noted there's a flexible linker(370-379) without density for modelling.
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: mucD, PA0766 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: G3XD20, peptidase Do
Has protein modificationN

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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: Cryo-EM Structure of a 24mer MucD cage / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1
Source (recombinant)Organism: Pseudomonas aeruginosa PAO1 (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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1200 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 40 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
SymmetryPoint symmetry: O (octahedral)
3D reconstructionResolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86270 / Symmetry type: POINT

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