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- EMDB-55005: Zuzalysin pentamer cryo-em -

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Basic information

Entry
Database: EMDB / ID: EMD-55005
TitleZuzalysin pentamer cryo-em
Map data
Sample
  • Complex: Zuzalysin
    • Protein or peptide: Zinc-dependent metalloprotease
  • Ligand: CALCIUM ION
  • Ligand: ZINC ION
  • Ligand: water
Keywordsmetallopeptidase / pentamer / 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: 2.38 Å
AuthorsRodriguez-Banqueri A / Gomis Ruth FX / Eckhard U / Potempa J / Glatt S / Koziej L / Madej M
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 4, 2025-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55005.png

Downloads & links

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Map

FileDownload / File: emd_55005.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 300 pix.
= 252. Å		0.84 Å/pix.
x 300 pix.
= 252. Å		0.84 Å/pix.
x 300 pix.
= 252. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.18086195 - 0.5296089
Average (Standard dev.)0.0026834707 (±0.02669696)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 251.99998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_55005_additional_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55005_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55005_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Zuzalysin

EntireName: Zuzalysin
Components
  • Complex: Zuzalysin
    • Protein or peptide: Zinc-dependent metalloprotease
  • Ligand: CALCIUM ION
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: Zuzalysin

SupramoleculeName: Zuzalysin / 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: 5 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 94.691438 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHENL YFQSKFDQTV AGAKKSEGPF TVYFTKKNEI LFAMPDSAFR REYLLSSRVA ATSNTREAVA GQMSTSPFLI KFSRDSINV YLHTPQVGAM VREDDPIVPS FKKNFFDPVL KAFPIVDTKD GKVLIDVTKF FREDEKSITP LTILPPTMQN A NVIKGMLD ...String:
MHHHHHHENL YFQSKFDQTV AGAKKSEGPF TVYFTKKNEI LFAMPDSAFR REYLLSSRVA ATSNTREAVA GQMSTSPFLI KFSRDSINV YLHTPQVGAM VREDDPIVPS FKKNFFDPVL KAFPIVDTKD GKVLIDVTKF FREDEKSITP LTILPPTMQN A NVIKGMLD PTASIVTEVK SFPRNVEIKS MLTYKTQPYS EPYTLIMQRS ILLLPEKPMR MRLQDNRVGI FNSSRQYFST DK DKVESFK LIHRWDLQPK DSAAYMRGEP VEPVKPIVFY VDSVFPDKWR ATIKQAIEDW RMAFEAAGFK NAIIAKDYPT KEE NPDFDP DDIRFSCFKY ATTTTANAMG PSFVDPRSGE IICADVIWYH NVLSLVHNWR FVQTGAVDPR VRKAVFDDEV MRES LRYVA AHEIGHTIGL MHNMGASYSF TIENLRDPQF TQKYGTTPSI MDYARNNFVA QPGDLERGVR LTPPIIGVYD IHAIN WAYR LVPGAKTAEE EKPTLNAWIA EKKDDPMFTF GAQQFPYTID PTDQTEDLSN DHFRAGDMSI SNLKIIAKNM DKWLLE KEA RYDDLRDMHG QLMSQYYRHV SHIMPYIGGV EHFEIRQGEE NTLSRRFITK DKQRKAMNWL LNQARTYRQW LAEPAFL NK VEQNSGMTDL LGKAMVAALF NPGSIGRIYE AEQSGQPGVY KLTDYANELI DAIFNVKGNL TDADRSIQNL AIDLMSAH S GLSTESKNTA RRLSEELDAL SHKLSEDNLP CALGCGGHHA AEDGADSFFR LTAFSKQAPN EVIAPLLLQQ LKRVQTIYR NRKATGNAAD RSFYDYQLLR LERLMKTN

UniProtKB: Zinc-dependent metalloprotease

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 10 / 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: 5 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 3033 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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 KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.88 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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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: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 59134
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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