9G7O | pdb_00009g7o

Crystal structure of Janthinobacterium lividum PE-like toxin, Jlx


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.247 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.209 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9G7O

This is version 1.2 of the entry. See complete history

Literature

Discovery of mono-ADP ribosylating toxins with high structural homology to Pseudomonas exotoxin A.

Masuyer, G.Taverner, A.MacKay, J.Lima Marques, A.R.Wang, Y.Hunter, T.Liu, K.Mrsny, R.J.

(2025) Commun Biol 8: 413-413

  • DOI: https://doi.org/10.1038/s42003-025-07845-y
  • Primary Citation Related Structures: 
    9G7M, 9G7N, 9G7O, 9G7P

  • PubMed Abstract: 

    Mono-ADP-ribosyl transferase (mART) proteins are secreted virulence factors produced by several human pathogens, the founding member being diphtheria toxin (DT). Pseudomonas aeruginosa can also secrete a mART toxin, known as exotoxin A (PE), but with an organization of its three functional domains (receptor, translocation, and enzymatic elements) that is opposite to DT. Two additional PE-like toxins (PLTs) have been identified from Vibrio cholerae and Aeromonas hydrophila, suggesting more PLT family members may exist. Database mining discovered six additional putative homologues, considerably extending this group of PLTs across a wide range of bacterial species. Here, we examine sequence and structural information for these new family members with respect to previously identified PLTs. The X-ray crystal structures of four new homologues show the conservation of critical features responsible for structure and function. This study shows the potential of these newly described toxins for the development of novel drug delivery platforms. Additionally, genomic analysis suggests horizontal gene transfer to account for the wide distribution of PLTs across a range of eubacteria species, highlighting the need to monitor emerging pathogens and their virulence factors.


  • Organizational Affiliation
    • Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden. geoffrey.masuyer@dbb.su.se.

Macromolecule Content 

  • Total Structure Weight: 272.95 kDa 
  • Atom Count: 20,731 
  • Modeled Residue Count: 2,457 
  • Deposited Residue Count: 2,468 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Janthinobacterium lividum PE-like toxin catalytically inactive mutant
A, B, C, D
617Janthinobacterium lividumMutation(s): 0 
EC: 2.4.2.36
UniProt
Find proteins for A0ACD6B8U3 (Janthinobacterium sp. B9-8)
Explore A0ACD6B8U3 
Go to UniProtKB:  A0ACD6B8U3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6B8U3
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P6G

Query on P6G



Download:Ideal Coordinates CCD File
J [auth B],
P [auth C]
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
E [auth A]
H [auth A]
K [auth B]
L [auth B]
Q [auth C]
E [auth A],
H [auth A],
K [auth B],
L [auth B],
Q [auth C],
R [auth C],
U [auth D],
V [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
O [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
IMD

Query on IMD



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
M [auth B],
S [auth C],
W [auth D]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
CL

Query on CL



Download:Ideal Coordinates CCD File
I [auth A],
N [auth B],
T [auth C],
X [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.247 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.209 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 224.625α = 90
b = 143.241β = 119.351
c = 110.67γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data

  • Released Date: 2025-01-29 
  • Deposition Author(s): Masuyer, G.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release
  • Version 1.1: 2025-03-19
    Changes: Database references
  • Version 1.2: 2025-03-26
    Changes: Database references