2Z64

Crystal structure of mouse TLR4 and mouse MD-2 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 
    0.290 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.242 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.244 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 2.2 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: https://doi.org/10.1016/j.cell.2007.08.002
  • Primary Citation of Related Structures:  
    2Z62, 2Z63, 2Z64, 2Z65, 2Z66

  • 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. 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Toll-like receptor 4599Mus musculusMutation(s): 0 
Gene Names: Tlr4
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9QUK6 (Mus musculus)
Explore Q9QUK6 
Go to UniProtKB:  Q9QUK6
IMPC:  MGI:96824
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9QUK6
Glycosylation
Glycosylation Sites: 9Go to GlyGen: Q9QUK6-1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Lymphocyte antigen 96B [auth C]135Mus musculusMutation(s): 0 
Gene Names: Md2
Membrane Entity: Yes 
UniProt
Find proteins for Q9JHF9 (Mus musculus)
Explore Q9JHF9 
Go to UniProtKB:  Q9JHF9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JHF9
Glycosylation
Glycosylation Sites: 3Go to GlyGen: Q9JHF9-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth B]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, E
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
F
4N/A
Glycosylation Resources
GlyTouCan:  G86566TX
GlyCosmos:  G86566TX
GlyGen:  G86566TX
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free:  0.290 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.242 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.244 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.158α = 90
b = 101.882β = 90
c = 126.364γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

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 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-10-23
    Changes: Structure summary