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- EMDB-55026: Zuzalysin active dodecahedral complex -

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Basic information

Entry
Database: EMDB / ID: EMD-55026
TitleZuzalysin active dodecahedral complex
Map data
Sample
  • Complex: Zuzalysin
    • Protein or peptide: Zinc-dependent metalloprotease
  • Ligand: CALCIUM ION
  • Ligand: ZINC ION
  • Ligand: water
Keywordsmetallopeptidase / dodecahedral complex / 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: 1.83 Å
AuthorsRodriguez-Banqueri A / Madej M / Eckhard U / Koziej L / Glatt S / Potempa J / Gomis Ruth FX
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of Zuzalysin active dodecahedral at 1.83 Angstroms resolution
Authors: Rodriguez-Banqueri A / Madej M / Eckhard U / Koziej L / Glatt S / Potempa J / Gomis-Ruth FX
History
DepositionSep 5, 2025-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55026.png

Downloads & links

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Map

FileDownload / File: emd_55026.map.gz / Format: CCP4 / Size: 476.8 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 500 pix.
= 420. Å		0.84 Å/pix.
x 500 pix.
= 420. Å		0.84 Å/pix.
x 500 pix.
= 420. 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-0.19480564 - 0.8408453
Average (Standard dev.)0.0074456036 (±0.053548235)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 420.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_55026_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55026_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55026_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: 60 / 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: 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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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 39048 / 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: 1.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 64886
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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