2Z65

Crystal structure of the human TLR4 TV3 hybrid-MD-2-Eritoran complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.289 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.238 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.240 (Depositor) 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted E55Click on this verticalbar to view detailsBest fitted NAGClick on this verticalbar to view details

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 4, Variable lymphocyte receptor B
A, B
276Homo sapiensEptatretus burgeri
This entity is chimeric
Mutation(s): 0 
Gene Names: TLR4VLRB.61
UniProt & NIH Common Fund Data Resources
Find proteins for O00206 (Homo sapiens)
Explore O00206 
Go to UniProtKB:  O00206
PHAROS:  O00206
GTEx:  ENSG00000136869 
Find proteins for Q4G1L2 (Eptatretus burgeri)
Explore Q4G1L2 
Go to UniProtKB:  Q4G1L2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ4G1L2O00206
Glycosylation
Glycosylation Sites: 2Go to GlyGen: O00206-1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Lymphocyte antigen 96
C, D
140Homo sapiensMutation(s): 0 
Gene Names: MD-2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6Y9 (Homo sapiens)
Explore Q9Y6Y9 
Go to UniProtKB:  Q9Y6Y9
PHAROS:  Q9Y6Y9
GTEx:  ENSG00000154589 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y6Y9
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
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
E
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
E55
Query on E55

Download Ideal Coordinates CCD File 
K [auth C],
L [auth D]
3-O-DECYL-2-DEOXY-6-O-{2-DEOXY-3-O-[(3R)-3-METHOXYDECYL]-6-O-METHYL-2-[(11Z)-OCTADEC-11-ENOYLAMINO]-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSYL}-2-[(3-OXOTETRADECANOYL)AMINO]-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE
C66 H126 N2 O19 P2
BPSMYQFMCXXNPC-MFCPCZTFSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth B],
I [auth B],
J [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
E55 BindingDB:  2Z65 IC50: 1.5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.289 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.238 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.240 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.192α = 90
b = 80.987β = 93.01
c = 107.762γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted E55Click on this verticalbar to view detailsBest 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 1.2: 2017-08-09
    Changes: Advisory, Refinement description, Source and taxonomy
  • 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: 2024-10-09
    Changes: Structure summary