2Z65 | pdb_00002z65

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), 0.282 (DCC) 
  • R-Value Work: 
    0.238 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 
    0.240 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 98.97 kDa 
  • Atom Count: 7,096 
  • Modeled Residue Count: 832 
  • Deposited Residue Count: 832 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  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
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Reference Sequence
Find similar proteins by:|  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 GlycosylationD 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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.289 (Depositor), 0.282 (DCC) 
  • R-Value Work:  0.238 (Depositor), 0.231 (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

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Ligand Structure Quality Assessment 


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