2Z63

Crystal structure of the TV8 hybrid of human TLR4 and hagfish VLRB.61


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.251 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystal Structure of the TLR4-MD-2 Complex with Bound Endotoxin Antagonist Eritoran

Kim, H.M.Park, B.S.Kim, J.-I.Kim, S.E.Lee, J.Oh, S.C.Enkhbayar, P.Matsushima, N.Lee, H.Yoo, O.J.Lee, J.-O.

(2007) Cell 130: 906-917

  • DOI: 10.1016/j.cell.2007.08.002
  • Primary Citation of Related Structures:  
    2Z66, 2Z62, 2Z63, 2Z64, 2Z65

  • PubMed Abstract: 
  • TLR4 and MD-2 form a heterodimer that recognizes LPS (lipopolysaccharide) from Gram-negative bacteria. Eritoran is an analog of LPS that antagonizes its activity by binding to the TLR4-MD-2 complex. We determined the structure of the full-length ectodomain of the mouse TLR4 and MD-2 complex ...

    TLR4 and MD-2 form a heterodimer that recognizes LPS (lipopolysaccharide) from Gram-negative bacteria. Eritoran is an analog of LPS that antagonizes its activity by binding to the TLR4-MD-2 complex. We determined the structure of the full-length ectodomain of the mouse TLR4 and MD-2 complex. We also produced a series of hybrids of human TLR4 and hagfish VLR and determined their structures with and without bound MD-2 and Eritoran. TLR4 is an atypical member of the LRR family and is composed of N-terminal, central, and C-terminal domains. The beta sheet of the central domain shows unusually small radii and large twist angles. MD-2 binds to the concave surface of the N-terminal and central domains. The interaction with Eritoran is mediated by a hydrophobic internal pocket in MD-2. Based on structural analysis and mutagenesis experiments on MD-2 and TLR4, we propose a model of TLR4-MD-2 dimerization induced by LPS.


    Organizational Affiliation

    Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejon, Korea 305-701.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Toll-like receptor 4, Variable lymphocyte receptor BA570Homo sapiensEptatretus burgeri
This entity is chimeric
Mutation(s): 0 
Gene Names: TLR4VLRB.61
EC: 3.2.2.6
Find proteins for O00206 (Homo sapiens)
Explore O00206 
Go to UniProtKB:  O00206
NIH Common Fund Data Resources
PHAROS:  O00206
Find proteins for Q4G1L2 (Eptatretus burgeri)
Explore Q4G1L2 
Go to UniProtKB:  Q4G1L2
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseB3 N-Glycosylation Oligosaccharides Interaction
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC2 N-Glycosylation Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.251 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.136α = 90
b = 88.136β = 90
c = 92.205γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-09-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-08-09
    Changes: Refinement description, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary