9SM4 | pdb_00009sm4

Zuzalysin active dodecahedral complex

• PDB DOI: https://doi.org/10.2210/pdb9SM4/pdb
• EM Map EMD-55026: EMDB EMDataResource

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


• Deposited: 2025-09-05 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

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 1.83 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of Zuzalysin active dodecahedral at 1.83 Angstroms resolution

Rodriguez-Banqueri, A., Madej, M., Eckhard, U., Koziej, L., Glatt, S., Potempa, J., Gomis-Ruth, F.X.

To be published.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 60-mer - A60 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 5,690.22 kDa 
• Atom Count: 419,328 
• Modeled Residue Count: 46,500 
• Deposited Residue Count: 49,680 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc-dependent metalloprotease	A [auth A1], AA [auth F2], AB [auth K3], B [auth A2], BA [auth F3], BB [auth K4], C [auth A3], CA [auth F4], CB [auth K5], D [auth A4], DA [auth F5], DB [auth L1], E [auth A5], EA [auth G1], EB [auth L2], F [auth B1], FA [auth G2], FB [auth L3], G [auth B2], GA [auth G3], GB [auth L4], H [auth B3], HA [auth G4], HB [auth L5], I [auth B4], IA [auth G5], J [auth B5], JA [auth H1], K [auth C1], KA [auth H2], L [auth C2], LA [auth H3], M [auth C3], MA [auth H4], N [auth C4], NA [auth H5], O [auth C5], OA [auth I1], P [auth D1], PA [auth I2], Q [auth D2], QA [auth I3], R [auth D3], RA [auth I4], S [auth D4], SA [auth I5], T [auth D5], TA [auth J1], U [auth E1], UA [auth J2], V [auth E2], VA [auth J3], W [auth E3], WA [auth J4], X [auth E4], XA [auth J5], Y [auth E5], YA [auth K1], Z [auth F1], ZA [auth K2]	828	Porphyromonas gingivalis	Mutation(s): 0  Gene Names: NY149_10785
UniProt
Find proteins for A0AAF0BD41 (Porphyromonas gingivalis) Explore A0AAF0BD41  Go to UniProtKB:  A0AAF0BD41

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	AD [auth C5], AG [auth I1], BE [auth E4], BH [auth J5], CC [auth B2], CF [auth G3], CI [auth L4], DD [auth D1], DG [auth I2], EE [auth E5], EH [auth K1], FC [auth B3], FF [auth G4], FI [auth L5], GD [auth D2], GG [auth I3], HE [auth F1], HH [auth K2], IC [auth B4], IF [auth G5], JD [auth D3], JG [auth I4], KB [auth A1], KE [auth F2], KH [auth K3], LC [auth B5], LF [auth H1], MD [auth D4], MG [auth I5], NB [auth A2], NE [auth F3], NH [auth K4], OC [auth C1], OF [auth H2], PD [auth D5], PG [auth J1], QB [auth A3], QE [auth F4], QH [auth K5], RC [auth C2], RF [auth H3], SD [auth E1], SG [auth J2], TB [auth A4], TE [auth F5], TH [auth L1], UC [auth C3], UF [auth H4], VD [auth E2], VG [auth J3], WB [auth A5], WE [auth G1], WH [auth L2], XC [auth C4], XF [auth H5], YD [auth E3], YG [auth J4], ZB [auth B1], ZE [auth G2], ZH [auth L3]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	AC [auth B2], AE [auth E4], AF [auth G3], AH [auth J5], AI [auth L4], BC [auth B2], BD [auth D1], BF [auth G3], BG [auth I2], BI [auth L4], CD [auth D1], CE [auth E5], CG [auth I2], CH [auth K1], DC [auth B3], DE [auth E5], DF [auth G4], DH [auth K1], DI [auth L5], EC [auth B3], ED [auth D2], EF [auth G4], EG [auth I3], EI [auth L5], FD [auth D2], FE [auth F1], FG [auth I3], FH [auth K2], GC [auth B4], GE [auth F1], GF [auth G5], GH [auth K2], HC [auth B4], HD [auth D3], HF [auth G5], HG [auth I4], IB [auth A1], ID [auth D3], IE [auth F2], IG [auth I4], IH [auth K3], JB [auth A1], JC [auth B5], JE [auth F2], JF [auth H1], JH [auth K3], KC [auth B5], KD [auth D4], KF [auth H1], KG [auth I5], LB [auth A2], LD [auth D4], LE [auth F3], LG [auth I5], LH [auth K4], MB [auth A2], MC [auth C1], ME [auth F3], MF [auth H2], MH [auth K4], NC [auth C1], ND [auth D5], NF [auth H2], NG [auth J1], OB [auth A3], OD [auth D5], OE [auth F4], OG [auth J1], OH [auth K5], PB [auth A3], PC [auth C2], PE [auth F4], PF [auth H3], PH [auth K5], QC [auth C2], QD [auth E1], QF [auth H3], QG [auth J2], RB [auth A4], RD [auth E1], RE [auth F5], RG [auth J2], RH [auth L1], SB [auth A4], SC [auth C3], SE [auth F5], SF [auth H4], SH [auth L1], TC [auth C3], TD [auth E2], TF [auth H4], TG [auth J3], UB [auth A5], UD [auth E2], UE [auth G1], UG [auth J3], UH [auth L2], VB [auth A5], VC [auth C4], VE [auth G1], VF [auth H5], VH [auth L2], WC [auth C4], WD [auth E3], WF [auth H5], WG [auth J4], XB [auth B1], XD [auth E3], XE [auth G2], XG [auth J4], XH [auth L3], YB [auth B1], YC [auth C5], YE [auth G2], YF [auth I1], YH [auth L3], ZC [auth C5], ZD [auth E4], ZF [auth I1], ZG [auth J5]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 1.83 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	2.0rc1_5617
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-16 
Deposition Author(s): Rodriguez-Banqueri, A., Madej, M., Eckhard, U., Koziej, L., Glatt, S., Potempa, J., Gomis Ruth, F.X.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-09-16
  Type: Initial release