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- PDB-24xx: Cryo-EM Structure of a 12mer MucD cage -

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Basic information

Entry
Database: PDB / ID: 24xx
TitleCryo-EM Structure of a 12mer 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: 5 Å
AuthorsJiang, Y.J. / Gao, Y.G.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: PLoS Biol / Year: 2026
Title: MucD regulates alginate biosynthesis through the proteolytic control of AlgX and AlgK in Pseudomonas aeruginosa.
Authors: Yujun Jiang / Xin-Fu Yan / Rya Ero / Chao Wang / Kanaga Sabapathy / Yong-Gui Gao /
Abstract: Pseudomonas aeruginosa is an opportunistic human pathogen capable of infecting a wide range of tissues and organs. Its persistence during chronic infection is strongly associated with biofilm ...Pseudomonas aeruginosa is an opportunistic human pathogen capable of infecting a wide range of tissues and organs. Its persistence during chronic infection is strongly associated with biofilm formation, which depends on extracellular polysaccharides such as alginate. The HtrA-like periplasmic serine protease MucD is a key regulator of bacterial virulence, stress response, and alginate production, yet its molecular mechanism has remained largely unclear. Here, we discovered the alginate acetylation and export proteins AlgX and AlgK as MucD substrates, and characterized their degradation by mass spectrometry and bioinformatic analysis. We further determined the cryo-EM structure of MucD bound to an AlgK-derived substrate peptide, offering atomic insights into MucD oligomerization assembly, substrate recognition, and specificity. Together with structure-guided mutagenesis and biochemical assays, our results revealed that MucD proteolytic activity is governed by an equilibrium between a resting 12-mer and an active trimer. Crucially, we demonstrate that MucD represses alginate biosynthesis post-translationally, in addition to its previously implicated role in transcriptional regulation. These findings define a distinct activation mechanism and regulatory function for MucD and provide new insight into bacterial HtrA-like serine proteases.
History
DepositionMar 24, 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
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Revision 1.1Sep 30, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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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
C: 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


Theoretical massNumber of molelcules
Total (without water)614,30912
Polymers614,30912
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.: 12 / Mutation: S217A
Source method: isolated from a genetically manipulated source
Details: All chains contain S217A mutation and 6*His tag at C-terminus.
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 12mer MucD cage / Type: COMPLEX / Details: Cryo-EM Structure of a 12mer MucD cage / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
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
3D reconstructionResolution: 5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 114738 / Symmetry type: POINT

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