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- PDB-9smj: Zuzalysin zymogen dodecahedral complex E439A -

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Basic information

Entry
Database: PDB / ID: 9smj
TitleZuzalysin zymogen dodecahedral complex E439A
ComponentsZinc-dependent metalloprotease
KeywordsHYDROLASE / metallopeptidase / dodecahedral complex / zymogen / prophyromonas gingivalis
Function / homology
Function and homology information


metallopeptidase activity
Similarity search - Function
EcxA, zinc-binding / Domain of unknown function DUF5117 / Domain of unknown function DUF5118 / Bacterial MMP-like domain / Domain of unknown function (DUF5117) / Domain of unknown function (DUF5118) / Met-zincin / Metallopeptidase, catalytic domain superfamily
Similarity search - Domain/homology
Zinc-dependent metalloprotease
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsRodriguez-Banqueri, A. / Madej, M. / Eckhard, U. / Potempa, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Angew Chem Int Ed Engl / Year: 2026
Title: Structure and Function of a Multi-Megadalton Virus-Like Proteolytic Dodecahedron.
Authors: Mariusz Madej / Arturo Rodríguez-Banqueri / Danuta Mizgalska / Borys Szmigielski / Zuzanna Nowakowska / Małgorzata Benedyk-Machaczka / Monika Bzowska / Katarzyna Mikruta / Juan Sebastián ...Authors: Mariusz Madej / Arturo Rodríguez-Banqueri / Danuta Mizgalska / Borys Szmigielski / Zuzanna Nowakowska / Małgorzata Benedyk-Machaczka / Monika Bzowska / Katarzyna Mikruta / Juan Sebastián Ramírez-Larrota / Chinanu Agunanne / Olivier Julien / Anthony J O'Donoghue / Carsten Scavenius / Mario López-Martín / Enrique Marcos / Łukasz Koziej / Sebastian Glatt / Pablo Guerra / Ulrich Eckhard / Jan Potempa / F Xavier Gomis-Rüth /
Abstract: Natural pentamer dodecahedra (Ddhs) span six orders of magnitude in diameter. Among proteins, only two catalytic Ddhs have been structurally characterized: lumazine synthase (LS) and the core of ...Natural pentamer dodecahedra (Ddhs) span six orders of magnitude in diameter. Among proteins, only two catalytic Ddhs have been structurally characterized: lumazine synthase (LS) and the core of pyruvate dehydrogenase (PDH). Zuzalysin (ZUZ) is a ≈95-kDa metallopeptidase secreted for virulence by Porphyromonas gingivalis. Calcium converts latent flexible monomers into active ≈0.5-MDa pentamers that further assemble hierarchically into bipentamers, tripentamers, and a ≈5.6-MDa, ≈355-Å virus-like dodecahedron (Ddh). Experimental structures (1.8-3.6 Å) across these states reveal the molecular basis of activation, association, and catalysis, culminating in Ddh, which is physiologic, exceeds small viral capsids, and has 20 main entry pores and 60 lumen-facing active sites. ZUZ represents the largest catalytic protein assembly resolved at high resolution, exceeding LS, PDH, and major peptidase complexes in size and/or resolution.
History
DepositionSep 8, 2025Deposition site: PDBE / Processing site: PDBE
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

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Assembly

Deposited unit
A1: Zinc-dependent metalloprotease
A2: Zinc-dependent metalloprotease
A3: Zinc-dependent metalloprotease
A4: Zinc-dependent metalloprotease
A5: Zinc-dependent metalloprotease
B1: Zinc-dependent metalloprotease
B2: Zinc-dependent metalloprotease
B3: Zinc-dependent metalloprotease
B4: Zinc-dependent metalloprotease
B5: Zinc-dependent metalloprotease
C1: Zinc-dependent metalloprotease
C2: Zinc-dependent metalloprotease
C3: Zinc-dependent metalloprotease
C4: Zinc-dependent metalloprotease
C5: Zinc-dependent metalloprotease
D1: Zinc-dependent metalloprotease
D2: Zinc-dependent metalloprotease
D3: Zinc-dependent metalloprotease
D4: Zinc-dependent metalloprotease
D5: Zinc-dependent metalloprotease
E1: Zinc-dependent metalloprotease
E2: Zinc-dependent metalloprotease
E3: Zinc-dependent metalloprotease
E4: Zinc-dependent metalloprotease
E5: Zinc-dependent metalloprotease
F1: Zinc-dependent metalloprotease
F2: Zinc-dependent metalloprotease
F3: Zinc-dependent metalloprotease
F4: Zinc-dependent metalloprotease
F5: Zinc-dependent metalloprotease
G1: Zinc-dependent metalloprotease
G2: Zinc-dependent metalloprotease
G3: Zinc-dependent metalloprotease
G4: Zinc-dependent metalloprotease
G5: Zinc-dependent metalloprotease
H1: Zinc-dependent metalloprotease
H2: Zinc-dependent metalloprotease
H3: Zinc-dependent metalloprotease
H4: Zinc-dependent metalloprotease
H5: Zinc-dependent metalloprotease
I1: Zinc-dependent metalloprotease
I2: Zinc-dependent metalloprotease
I3: Zinc-dependent metalloprotease
I4: Zinc-dependent metalloprotease
I5: Zinc-dependent metalloprotease
J1: Zinc-dependent metalloprotease
J2: Zinc-dependent metalloprotease
J3: Zinc-dependent metalloprotease
J4: Zinc-dependent metalloprotease
J5: Zinc-dependent metalloprotease
K1: Zinc-dependent metalloprotease
K2: Zinc-dependent metalloprotease
K3: Zinc-dependent metalloprotease
K4: Zinc-dependent metalloprotease
K5: Zinc-dependent metalloprotease
L1: Zinc-dependent metalloprotease
L2: Zinc-dependent metalloprotease
L3: Zinc-dependent metalloprotease
L4: Zinc-dependent metalloprotease
L5: Zinc-dependent metalloprotease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,834,932240
Polymers5,826,19860
Non-polymers8,734180
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Zinc-dependent metalloprotease


Mass: 97103.305 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: NY149_10785 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AAF0BD41
#2: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 120 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: Zn / 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: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Zuzalysin zymogen dodecahedral complex E439A / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: OTHER / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2700 nm / Nominal defocus min: 1700 nm
Image recordingElectron dose: 38.58 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX2.0rc1_5617model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36983 / Symmetry type: POINT
RefinementCross valid method: NONE

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