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 9SMJ | pdb_00009smj

Zuzalysin zymogen dodecahedral complex E439A


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.64 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9SMJ

This is version 1.0 of the entry. See complete history. 

Literature

Structure and Function of a Multi-Megadalton Virus-Like Proteolytic Dodecahedron.

Madej, M., Rodriguez-Banqueri, A., Mizgalska, D., Szmigielski, B., Nowakowska, Z., Benedyk-Machaczka, M., Bzowska, M., Mikruta, K., Ramirez-Larrota, J.S., Agunanne, C., Julien, O., O'Donoghue, A.J., Scavenius, C., Lopez-Martin, M., Marcos, E., Koziej, L., Glatt, S., Guerra, P., Eckhard, U., Potempa, J., Gomis-Ruth, F.X.

(2026) Angew Chem Int Ed Engl : e5597279-e5597279

  • DOI: https://doi.org/10.1002/anie.5597279
  • Primary Citation Related Structures: 
    9SLL, 9SLN, 9SM4, 9SM8, 9SMJ

  • PubMed 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 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 ZUZ ). Experimental structures (1.8-3.6 Å) across these states reveal the molecular basis of activation, association, and catalysis, culminating in Ddh ZUZ , 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.


  • Organizational Affiliation: 
    • Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland.

Macromolecule Content 

  • Total Structure Weight: 5,834.93 kDa 
  • Atom Count: 394,860 
  • Modeled Residue Count: 49,080 
  • Deposited Residue Count: 51,120 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Zinc-dependent metalloprotease852Porphyromonas gingivalisMutation(s): 0 
Gene Names: NY149_10785
UniProt
Find proteins for A0AAF0BD41 (Porphyromonas gingivalis)
Explore A0AAF0BD41 
Go to UniProtKB:  A0AAF0BD41
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AAF0BD41
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
AD [auth C5]
AG [auth I1]
BE [auth E4]
BH [auth J5]
CC [auth B2]
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)

Query on CA



Download:Ideal Coordinates CCD File
AC [auth B2]
AE [auth E4]
AF [auth G3]
AH [auth J5]
AI [auth L4]
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: 2.64 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX2.0rc1_5617
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-23
    Type: Initial release