9IB7 | pdb_00009ib7

Tumor necrosis factor-like lectin PLTL from Photorhabdus laumondii in complex with Blood group B trisaccharide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.199 (Depositor), 0.199 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.174 (DCC) 

Starting Model: experimental
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Literature

Structural and functional characterization of the newly identified Photorhabdus laumondii tumor necrosis factor-like lectin.

Melicher, F.Dobes, P.Komarek, J.Faltinek, L.Korsak, M.Sykorova, P.Houser, J.Wimmerova, M.

(2025) FEBS J 

  • DOI: https://doi.org/10.1111/febs.70293
  • Primary Citation of Related Structures:  
    9IB6, 9IB7, 9IB8, 9IB9

  • PubMed Abstract: 

    Photorhabdus bacteria live in mutualistic relationships with Heterorhabditis nematodes, and together, they act as effective insect pathogens. These bacteria produce a diverse array of lectins, sugar-binding proteins that are believed to play crucial roles in the complex tripartite interaction among Photorhabdus, nematodes, and their insect hosts. One such lectin, Photorhabdus laumondii tumor necrosis factor (TNF)-like lectin (PLTL), identified in Photorhabdus laumondii subsp. laumondii TTO1, exhibits notable sequence similarity to the N-terminal domain of the BC2L-C lectin (BC2L-CN), a TNF-like lectin recognized for its specificity toward fucosylated glycans associated with human embryonic stem cells and certain cancers. Through glycan array analysis and surface plasmon resonance, we identified PLTL's binding preference for branched histo-blood group oligosaccharides. The crystallographic structure of PLTL in complex with the BLe b pentasaccharide reveals a network of direct and water-mediated hydrogen bonds simultaneously stabilizing the Fucα1-2 and Galα1-3 moieties, which define its narrow glycan specificity. A combination of mass spectrometry, protein crystallography, and analytical ultracentrifugation showed a unique hexameric PLTL architecture stabilized by intermolecular disulfide bridges. Our data suggest that PLTL may contribute to the mutualistic relationship between Photorhabdus and its nematode symbiont, Heterorhabditis bacteriophora, rather than playing a role in the interaction with the insect host. This study provides a structural and functional characterization of PLTL, a newly identified member of the TNF-like lectin family. Comparative analysis with BC2L-CN highlights both conserved and distinct structural features, suggesting potential applications in glycan recognition-based diagnostics or biotechnological tools beyond its biological role. Our findings underscore its complex glycan specificity and offer insights into its potential role in Photorhabdus-nematode symbiosis.


  • Organizational Affiliation
    • Central European Institute of Technology (CEITEC), Masaryk University, Brno, 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 15/17
A, B, C
139Photorhabdus laumondii subsp. laumondii TTO1Mutation(s): 0 
Gene Names: plu4240
UniProt
Find proteins for Q7MZP1 (Photorhabdus laumondii subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01))
Explore Q7MZP1 
Go to UniProtKB:  Q7MZP1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7MZP1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]beta-D-galactopyranoseD [auth E],
E [auth H]
3N/A
Glycosylation Resources
GlyTouCan:  G47548GA
GlyCosmos:  G47548GA
GlyGen:  G47548GA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.199 (Depositor), 0.199 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.174 (DCC) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.823α = 90
b = 81.823β = 90
c = 112.777γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLM2023042

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-29
    Type: Initial release