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- PDB-9sm4: Zuzalysin active dodecahedral complex -

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Basic information

Entry
Database: PDB / ID: 9sm4
TitleZuzalysin active dodecahedral complex
ComponentsZinc-dependent metalloprotease
KeywordsHYDROLASE / metallopeptidase / dodecahedral complex / 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: 1.83 Å
AuthorsRodriguez-Banqueri, A. / Madej, M. / Eckhard, U. / Koziej, L. / Glatt, S. / Potempa, J. / Gomis Ruth, F.X.
Funding support1items
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, F.X.
History
DepositionSep 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 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

Downloads & links

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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)5,690,220240
Polymers5,681,48660
Non-polymers8,734180
Water703,45039048
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: 94691.438 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39048 / Source method: isolated from a natural source / Formula: H2O
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 / 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

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2100 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 40.88 e/Å2 / Film or detector model: FEI FALCON III (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: 1.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 64886 / Symmetry type: POINT

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