5IJC

The crystal structure of mouse TLR4/MD-2/neoseptin-3 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

TLR4/MD-2 activation by a synthetic agonist with no similarity to LPS.

Wang, Y.Su, L.Morin, M.D.Jones, B.T.Whitby, L.R.Surakattula, M.M.Huang, H.Shi, H.Choi, J.H.Wang, K.W.Moresco, E.M.Berger, M.Zhan, X.Zhang, H.Boger, D.L.Beutler, B.

(2016) Proc.Natl.Acad.Sci.USA 113: E884-E893

  • DOI: 10.1073/pnas.1525639113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Structurally disparate molecules reportedly engage and activate Toll-like receptor (TLR) 4 and other TLRs, yet the interactions that mediate binding and activation by dissimilar ligands remain unknown. We describe Neoseptins, chemically synthesized p ...

    Structurally disparate molecules reportedly engage and activate Toll-like receptor (TLR) 4 and other TLRs, yet the interactions that mediate binding and activation by dissimilar ligands remain unknown. We describe Neoseptins, chemically synthesized peptidomimetics that bear no structural similarity to the established TLR4 ligand, lipopolysaccharide (LPS), but productively engage the mouse TLR4 (mTLR4)/myeloid differentiation factor 2 (MD-2) complex. Neoseptin-3 activates mTLR4/MD-2 independently of CD14 and triggers canonical myeloid differentiation primary response gene 88 (MyD88)- and Toll-interleukin 1 receptor (TIR) domain-containing adaptor inducing IFN-beta (TRIF)-dependent signaling. The crystal structure mTLR4/MD-2/Neoseptin-3 at 2.57-Å resolution reveals that Neoseptin-3 binds as an asymmetrical dimer within the hydrophobic pocket of MD-2, inducing an active receptor complex similar to that induced by lipid A. However, Neoseptin-3 and lipid A form dissimilar molecular contacts to achieve receptor activation; hence strong TLR4/MD-2 agonists need not mimic LPS.


    Organizational Affiliation

    Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Toll-like receptor 4, Variable lymphocyte receptor B chimera
A, B
594Mus musculusEptatretus burgeri
This entity is chimeric
Gene Names: Tlr4 (Lps), VLRB
Find proteins for Q9QUK6 (Mus musculus)
Go to UniProtKB:  Q9QUK6
Find proteins for Q4G1L2 (Eptatretus burgeri)
Go to UniProtKB:  Q4G1L2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Lymphocyte antigen 96
C, D
150Mus musculusGene Names: Ly96 (Esop1, Md2)
Find proteins for Q9JHF9 (Mus musculus)
Go to UniProtKB:  Q9JHF9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
61S
Query on 61S

Download SDF File 
Download CCD File 
A, B, D
tert-butyl (2R)-2-({4-amino-3-[2-(4-hydroxyphenyl)ethyl]benzoyl}amino)-4-phenylbutanoate
C29 H34 N2 O4
OACODUCFPHHCIH-AREMUKBSSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 70.752α = 90.00
b = 148.559β = 98.30
c = 131.720γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data scaling
PHASERphasing
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-05-04
    Type: Database references