2F2L

Crystal structure of tracheal cytotoxin (TCT) bound to the ectodomain complex of peptidoglycan recognition proteins LCa (PGRP-LCa) and LCx (PGRP-LCx)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of tracheal cytotoxin in complex with a heterodimeric pattern-recognition receptor.

Chang, C.I.Chelliah, Y.Borek, D.Mengin-Lecreulx, D.Deisenhofer, J.

(2006) Science 311: 1761-1764

  • DOI: 10.1126/science.1123056

  • PubMed Abstract: 
  • Tracheal cytotoxin (TCT), a naturally occurring fragment of Gram-negative peptidoglycan, is a potent elicitor of innate immune responses in Drosophila. It induces the heterodimerization of its recognition receptors, the peptidoglycan recognition prot ...

    Tracheal cytotoxin (TCT), a naturally occurring fragment of Gram-negative peptidoglycan, is a potent elicitor of innate immune responses in Drosophila. It induces the heterodimerization of its recognition receptors, the peptidoglycan recognition proteins (PGRPs) LCa and LCx, which activates the immune deficiency pathway. The crystal structure at 2.1 angstrom resolution of TCT in complex with the ectodomains of PGRP-LCa and PGRP-LCx shows that TCT is bound to and presented by the LCx ectodomain for recognition by the LCa ectodomain; the latter lacks a canonical peptidoglycan-docking groove conserved in other PGRPs. The interface, revealed in atomic detail, between TCT and the receptor complex highlights the importance of the anhydro-containing disaccharide in bridging the two ectodomains together and the critical role of diaminopimelic acid as the specificity determinant for PGRP interaction.


    Organizational Affiliation

    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Road, Dallas, TX 75390-9050, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidoglycan-recognition protein-LC isoform LCa
A
167Drosophila melanogasterMutation(s): 0 
Gene Names: PGRP-LC (ird7, PGRPLC)
Find proteins for Q9GNK5 (Drosophila melanogaster)
Go to UniProtKB:  Q9GNK5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Peptidoglycan recognition protein-LC isoform LCx
X
167Drosophila melanogasterMutation(s): 0 
Gene Names: PGRP-LC (ird7, PGRPLC)
Find proteins for Q9GNK5 (Drosophila melanogaster)
Go to UniProtKB:  Q9GNK5
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
X
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, X
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
HSQ
Query on HSQ

Download SDF File 
Download CCD File 
A
2-(acetylamino)-2-deoxy-alpha-L-idopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-SLBCVNJHSA-N
 Ligand Interaction
MLD
Query on MLD

Download SDF File 
Download CCD File 
X
GLCNAC(BETA1-4)-MURNAC(1,6-ANHYDRO)-L-ALA-GAMMA-D-GLU-MESO-A2PM-D-ALA
2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE(BETA1-4)-2-ACETAMIDO-1,6-ANHYDRO-3-O-[(R)-1-CARBOXYETHYL]-2-DEOXY-BETA-D-GLUCOPYRANOSE-L-ALANYL-GAMMA-D-GLUTAMYL-MESO-DIAMINOPIMELYL-D-ALANINE
C37 H59 N7 O20
UPFMKPIBAIPLHT-RSJSDIDPSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 41.123α = 90.00
b = 79.695β = 90.00
c = 114.389γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-04-04
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2011-10-05
    Type: Derived calculations