Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 180.25 kDa 
• Atom Count: 12500 
• Modelled Residue Count: 1482 
• Deposited Residue Count: 1494 
• Unique protein chains: 2

3FXI

Crystal structure of the human TLR4-human MD-2-E.coli LPS Ra complex

• DOI: 10.2210/pdb3FXI/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2009-01-21 Released: 2009-03-03 
• Deposition Author(s): Park, B.S., Song, D.H., Kim, H.M., Lee, J.-O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.281 
• R-Value Work: 0.241 

Literature

The structural basis of lipopolysaccharide recognition by the TLR4-MD-2 complex

Park, B.S., Song, D.H., Kim, H.M., Choi, B.-S., Lee, H., Lee, J.-O.

(2009) Nature 458: 1191-1195

• PubMed: 19252480 
• DOI: 10.1038/nature07830
• Primary Citation of Related Structures:  
  3FXI


• PubMed Abstract: 
  

The lipopolysaccharide (LPS) of Gram negative bacteria is a well-known inducer of the innate immune response. Toll-like receptor (TLR) 4 and myeloid differentiation factor 2 (MD-2) form a heterodimer that recognizes a common 'pattern' in structurally diverse LPS molecules. To understand the ligand specificity and receptor activation mechanism of the TLR4-MD-2-LPS complex we determined its crystal structure. LPS binding induced the formation of an m-shaped receptor multimer composed of two copies of the TLR4-MD-2-LPS complex arranged symmetrically. LPS interacts with a large hydrophobic pocket in MD-2 and directly bridges the two components of the multimer. Five of the six lipid chains of LPS are buried deep inside the pocket and the remaining chain is exposed to the surface of MD-2, forming a hydrophobic interaction with the conserved phenylalanines of TLR4. The F126 loop of MD-2 undergoes localized structural change and supports this core hydrophobic interface by making hydrophilic interactions with TLR4. Comparison with the structures of tetra-acylated antagonists bound to MD-2 indicates that two other lipid chains in LPS displace the phosphorylated glucosamine backbone by approximately 5 A towards the solvent area. This structural shift allows phosphate groups of LPS to contribute to receptor multimerization by forming ionic interactions with a cluster of positively charged residues in TLR4 and MD-2. The TLR4-MD-2-LPS structure illustrates the remarkable versatility of the ligand recognition mechanisms employed by the TLR family, which is essential for defence against diverse microbial infection.

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Organizational Affiliation: 

Department of Chemistry, KAIST, Daejeon, 305-701, Korea.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toll-like receptor 4	A, B	605	Homo sapiens	Mutation(s): 0  Gene Names: TLR4 EC: 3.2.2.6
UniProt & NIH Common Fund Data Resources
Find proteins for O00206 (Homo sapiens) Explore O00206  Go to UniProtKB:  O00206
PHAROS:  O00206 GTEx:  ENSG00000136869

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lymphocyte antigen 96	C, D	142	Homo sapiens	Mutation(s): 0  Gene Names: ESOP1, LY96, MD-2, MD2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6Y9 (Homo sapiens) Explore Q9Y6Y9  Go to UniProtKB:  Q9Y6Y9
PHAROS:  Q9Y6Y9 GTEx:  ENSG00000154589

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
L-glycero-alpha-D-manno-heptopyranose-(1-7)-L-glycero-alpha-D-manno-heptopyranose-(1-3)-L-glycero-alpha-D-manno-heptopyranose-(1-5)-[3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)]3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-alpha-D-glucopyranose-(1-6)-2-amino-2-deoxy-alpha-D-glucopyranose	E	7		N/A
Glycosylation Resources
GlyTouCan:  G75876QI GlyCosmos:  G75876QI

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, G, I, J	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
L-glycero-alpha-D-manno-heptopyranose-(1-7)-L-glycero-alpha-D-manno-heptopyranose-(1-3)-L-glycero-alpha-D-manno-heptopyranose-(1-5)-[3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)]3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-alpha-D-glucopyranose	H	7		N/A
Glycosylation Resources
GlyTouCan:  G02042LC GlyCosmos:  G02042LC

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FTT (Subject of Investigation/LOI)	AA [auth B], BA [auth B], K [auth A], L [auth A], M [auth A], N [auth A], Y [auth B], Z [auth B]	3-HYDROXY-TETRADECANOIC ACID C14 H28 O3 ATRNZOYKSNPPBF-CYBMUJFWSA-N
MYR (Subject of Investigation/LOI)	DA [auth B], P [auth A]	MYRISTIC ACID C14 H28 O2 TUNFSRHWOTWDNC-UHFFFAOYSA-N
NAG (Subject of Investigation/LOI)	IA [auth B], JA [auth B], KA [auth B], MA [auth C], NA [auth D], U [auth A], V [auth A], W [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
DAO (Subject of Investigation/LOI)	CA [auth B], O [auth A]	LAURIC ACID C12 H24 O2 POULHZVOKOAJMA-UHFFFAOYSA-N
PO4	EA [auth B], FA [auth B], GA [auth B], HA [auth B], Q [auth A], R [auth A], S [auth A], T [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	LA [auth B], X [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.281 
• R-Value Work: 0.241 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.16	α = 90
b = 103.5	β = 90
c = 251.81	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
DNA	data collection
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2009-01-21 
• Released Date: 2009-03-03 
Deposition Author(s): Park, B.S., Song, D.H., Kim, H.M., Lee, J.-O.

Revision History  

• Version 1.0: 2009-03-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2012-06-20
  Changes: Non-polymer description
• Version 1.3: 2020-07-01
  Changes: Advisory, Data collection, Derived calculations
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary