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- EMDB-55035: Zuzalysin zymogen dodecahedral complex E439A -

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Basic information

Entry
Database: EMDB / ID: EMD-55035
TitleZuzalysin zymogen dodecahedral complex E439A
Map data
Sample
  • Complex: Zuzalysin zymogen dodecahedral complex E439A
    • Protein or peptide: Zinc-dependent metalloprotease
  • Ligand: CALCIUM ION
  • Ligand: ZINC ION
Keywordsmetallopeptidase / dodecahedral complex / zymogen / prophyromonas gingivalis / HYDROLASE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsRodriguez-Banqueri A / Madej M / Eckhard U / Potempa J / Gomis Ruth FX / Koziej L
Funding support1 items
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, 2025-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55035.png

Downloads & links

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Map

FileDownload / File: emd_55035.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 400 pix.
= 372. Å		0.93 Å/pix.
x 400 pix.
= 372. Å		0.93 Å/pix.
x 400 pix.
= 372. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.08430822 - 0.35381007
Average (Standard dev.)0.013023277 (±0.039226882)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 372.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_55035_additional_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_55035_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55035_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Zuzalysin zymogen dodecahedral complex E439A

EntireName: Zuzalysin zymogen dodecahedral complex E439A
Components
  • Complex: Zuzalysin zymogen dodecahedral complex E439A
    • Protein or peptide: Zinc-dependent metalloprotease
  • Ligand: CALCIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: Zuzalysin zymogen dodecahedral complex E439A

SupramoleculeName: Zuzalysin zymogen dodecahedral complex E439A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Porphyromonas gingivalis (bacteria)

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Macromolecule #1: Zinc-dependent metalloprotease

MacromoleculeName: Zinc-dependent metalloprotease / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 97.103305 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MASMTGGQMG QSDYFFRSKK KKPATEAPAQ KSKFDQTVAG AKKSEGPFTV YFTKKNEILF AMPDSAFRRE YLLSSRVAAT SNTREAVAG QMSTSPFLIK FSRDSINVYL HTPQVGAMVR EDDPIVPSFK KNFFDPVLKA FPIVDTKDGK VLIDVTKFFR E DEKSITPL ...String:
MASMTGGQMG QSDYFFRSKK KKPATEAPAQ KSKFDQTVAG AKKSEGPFTV YFTKKNEILF AMPDSAFRRE YLLSSRVAAT SNTREAVAG QMSTSPFLIK FSRDSINVYL HTPQVGAMVR EDDPIVPSFK KNFFDPVLKA FPIVDTKDGK VLIDVTKFFR E DEKSITPL TILPPTMQNA NVIKGMLDPT ASIVTEVKSF PRNVEIKSML TYKTQPYSEP YTLIMQRSIL LLPEKPMRMR LQ DNRVGIF NSSRQYFSTD KDKVESFKLI HRWDLQPKDS AAYMRGEPVE PVKPIVFYVD SVFPDKWRAT IKQAIEDWRM AFE AAGFKN AIIAKDYPTK EENPDFDPDD IRFSCFKYAT TTTANAMGPS FVDPRSGEII CADVIWYHNV LSLVHNWRFV QTGA VDPRV RKAVFDDEVM RESLRYVAAH AIGHTIGLMH NMGASYSFTI ENLRDPQFTQ KYGTTPSIMD YARNNFVAQP GDLER GVRL TPPIIGVYDI HAINWAYRLV PGAKTAEEEK PTLNAWIAEK KDDPMFTFGA QQFPYTIDPT DQTEDLSNDH FRAGDM SIS NLKIIAKNMD KWLLEKEARY DDLRDMHGQL MSQYYRHVSH IMPYIGGVEH FEIRQGEENT LSRRFITKDK QRKAMNW LL NQARTYRQWL AEPAFLNKVE QNSGMTDLLG KAMVAALFNP GSIGRIYEAE QSGQPGVYKL TDYANELIDA IFNVKGNL T DADRSIQNLA IDLMSAHSGL STESKNTARR LSEELDALSH KLSEDNLPCA LGCGGHHAAE DGADSFFRLT AFSKQAPNE VIAPLLLQQL KRVQTIYRNR KATGNAADRS FYDYQLLRLE RLMKTNHHHH HH

UniProtKB: Zinc-dependent metalloprotease

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 120 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 60 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 38.58 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.7 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 36983
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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