8Q82 | pdb_00008q82

Photorhabdus laumondii lectin PLL4 in complex with alpha-methyl-fucoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.240 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.212 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The insight into the biology of five homologous lectins produced by the entomopathogenic bacterium and nematode symbiont Photorhabdus laumondii.

Paulenova, E.Dobes, P.Melicher, F.Houser, J.Faltinek, L.Hyrsl, P.Wimmerova, M.

(2025) Glycobiology 

  • DOI: https://doi.org/10.1093/glycob/cwaf033
  • Primary Citation of Related Structures:  
    8Q7U, 8Q80, 8Q81, 8Q82, 8Q83

  • PubMed Abstract: 

    Photorhabdus laumondii is a well-known bacterium with a complex life cycle involving mutualism with nematodes of the genus Heterorhabditis and pathogenicity towards insect hosts. It provides an excellent model for studying the diverse roles of lectins, saccharide-binding proteins, in both symbiosis and pathogenicity. This study focuses on the seven-bladed β-propeller lectins of P. laumondii (PLLs), examining their biochemical properties (structure and saccharide specificity) and biological functions (gene expression, interactions with the nematode symbiont, and the host immune system response). Structural analyses revealed diverse oligomeric states among PLLs and a unique organisation of binding sites not described outside the PLL lectin family. Lectins exhibited high specificity for fucosylated and O-methylated saccharides with a significant avidity effect for multivalent ligands. Gene expression analysis across bacterial growth phases revealed that PLLs are predominantly expressed during the exponential phase. Interaction studies with the host immune system demonstrated that PLL5 uniquely induced melanisation in Galleria mellonella hemolymph. Furthermore, PLL2, PLL3, and PLL5 interfered with reactive oxygen species production in human blood cells, indicating their potential role in modulating host immune responses. Biofilm formation assays and binding studies with nematode life stages showed no significant involvement of PLLs in nematode colonization. Our findings highlight the primary role of PLLs in Photorhabdus pathogenicity rather than in symbiosis and offer valuable insight into the fascinating dynamics within the Photorhabdus-nematode-insect triparted system.


  • Organizational Affiliation

    Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno 625 00, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 3/17
A, B
369Photorhabdus laumondii subsp. laumondii TTO1Mutation(s): 0 
Gene Names: plu0736
UniProt
Find proteins for Q7N8I6 (Photorhabdus laumondii subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01))
Explore Q7N8I6 
Go to UniProtKB:  Q7N8I6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7N8I6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MFU (Subject of Investigation/LOI)
Query on MFU

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
H [auth B]
methyl alpha-L-fucopyranoside
C7 H14 O5
OHWCAVRRXKJCRB-CXNFULCWSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.240 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.212 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.013α = 90
b = 82.859β = 105.357
c = 70.3γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Grant Agency of the Czech RepublicCzech Republic21-29622S

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release
  • Version 1.1: 2025-06-11
    Changes: Database references