9SLL | pdb_00009sll

Zuzalysin active pentamer

PDB DOI: https://doi.org/10.2210/pdb9SLL/pdb
EM Map EMD-55005: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Porphyromonas gingivalis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-09-04 Released: 2026-09-16
Deposition Author(s): Rodriguez-Banqueri, A., Madej, M., Eckhard, U., Koziej, L., Glatt, S., Potempa, J., Gomis Ruth, F.X.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.38 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structure and Function of a Multi-Megadalton Virus-Like Proteolytic Dodecahedron.

Madej, M., Rodriguez-Banqueri, A., Mizgalska, D., Szmigielski, B., Nowakowska, Z., Benedyk-Machaczka, M., Bzowska, M., Mikruta, K., Ramirez-Larrota, J.S., Agunanne, C., Julien, O., O'Donoghue, A.J., Scavenius, C., Lopez-Martin, M., Marcos, E., Koziej, L., Glatt, S., Guerra, P., Eckhard, U., Potempa, J., Gomis-Ruth, F.X.

(2026) Angew Chem Int Ed Engl : e5597279-e5597279

PubMed: 42723362 Search on PubMed
DOI: https://doi.org/10.1002/anie.5597279
Primary Citation Related Structures:
9SLL, 9SLN, 9SM4, 9SM8, 9SMJ

PubMed 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 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 _ZUZ). Experimental structures (1.8-3.6 Å) across these states reveal the molecular basis of activation, association, and catalysis, culminating in Ddh _ZUZ, 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.

Organizational Affiliation

Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland.

Macromolecule Content

Total Structure Weight: 474.19 kDa
Atom Count: 34,563
Modeled Residue Count: 3,880
Deposited Residue Count: 4,140
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc-dependent metalloprotease	A, B, C, D, E	828	Porphyromonas gingivalis	Mutation(s): 0 Gene Names: NY149_10785
UniProt
Find proteins for A0AAF0BD41 (Porphyromonas gingivalis) Explore A0AAF0BD41 Go to UniProtKB: A0AAF0BD41
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0AAF0BD41
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain T [auth E] SDF format, chain Q [auth D] SDF format, chain N [auth C] SDF format, chain K [auth B] SDF format, chain H [auth A] MOL2 format, chain T [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain N [auth C] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] mmCIF format, chain T [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain N [auth C] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A]	H [auth A], K [auth B], N [auth C], Q [auth D], T [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain T [auth E] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain T [auth E]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain S [auth E] SDF format, chain R [auth E] SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain S [auth E] MOL2 format, chain R [auth E] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain S [auth E] mmCIF format, chain R [auth E] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] I [auth B] J [auth B] L [auth C] F [auth A], G [auth A], I [auth B], J [auth B], L [auth C], M [auth C], O [auth D], P [auth D], R [auth E], S [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain R [auth E] Focus chain S [auth E] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain R [auth E] Focus chain S [auth E]