2XZ4

Crystal structure of the LFZ ectodomain of the peptidoglycan recognition protein LF

• PDB DOI: https://doi.org/10.2210/pdb2XZ4/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Drosophila melanogaster
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2010-11-23 Released: 2011-04-13 
• Deposition Author(s): Basbous, N., Coste, F., Leone, P., Vincentelli, R., Royet, J., Kellenberger, C., Roussel, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.201 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 

Literature

The Drosophila Peptidoglycan-Recognition Protein Lf Interacts with Peptidoglycan-Recognition Protein Lc to Downregulate the Imd Pathway.

Basbous, N., Coste, F., Leone, P., Vincentelli, R., Royet, J., Kellenberger, C., Roussel, A.

(2011) EMBO Rep 12: 327

• PubMed: 21372849 
• DOI: https://doi.org/10.1038/embor.2011.19
• Primary Citation of Related Structures:  
  2XZ4, 2XZ8


• PubMed Abstract: 
  

  The peptidoglycan (PGN)-recognition protein LF (PGRP-LF) is a specific negative regulator of the immune deficiency (Imd) pathway in Drosophila. We determine the crystal structure of the two PGRP domains constituting the ectodomain of PGRP-LF at 1.72 and 1.94 Å resolution. The structures show that the LFz and LFw domains do not have a PGN-docking groove that is found in other PGRP domains, and they cannot directly interact with PGN, as confirmed by biochemical-binding assays. By using surface plasmon resonance analysis, we show that the PGRP-LF ectodomain interacts with the PGRP-LCx ectodomain in the absence and presence of tracheal cytotoxin. Our results suggest a mechanism for downregulation of the Imd pathway on the basis of the competition between PRGP-LCa and PGRP-LF to bind to PGRP-LCx.

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Organizational Affiliation: 

Centre de Biophysique Moléculaire, UPR 4301 CNRS, Rue Charles Sadron, Orléans 2 45071, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.7 kDa 
• Atom Count: 2,877 
• Modelled Residue Count: 326 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDOGLYCAN-RECOGNITION PROTEIN LF	A, B	180	Drosophila melanogaster	Mutation(s): 0
UniProt
Find proteins for Q8SXQ7 (Drosophila melanogaster) Explore Q8SXQ7  Go to UniProtKB:  Q8SXQ7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PG	F [auth A]	2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL C11 H24 O6 SLNYBUIEAMRFSZ-UHFFFAOYSA-N
CU	C [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], G [auth B], H [auth B], I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.201 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.802	α = 90
b = 113.443	β = 90
c = 37.532	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-13 
Deposition Author(s): Basbous, N., Coste, F., Leone, P., Vincentelli, R., Royet, J., Kellenberger, C., Roussel, A.

Revision History  

• Version 1.0: 2011-04-13
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description