RCSB PDB - 4G8A: Crystal structure of human TLR4 polymorphic variant D299G and T399I in complex with MD-2 and LPS (original) (raw)

Crystal structure of human TLR4 polymorphic variant D299G and T399I in complex with MD-2 and LPS

This is version 2.2 of the entry. See complete history.

Structural analyses of human Toll-like receptor 4 polymorphisms D299G and T399I

[Ohto, U.](/search?q=citation.rcsb%5Fauthors:Ohto, U.), [Yamakawa, N.](/search?q=citation.rcsb%5Fauthors:Yamakawa, N.), [Akashi-Takamura, S.](/search?q=citation.rcsb%5Fauthors:Akashi-Takamura, S.), [Miyake, K.](/search?q=citation.rcsb%5Fauthors:Miyake, K.), [Shimizu, T.](/search?q=citation.rcsb%5Fauthors:Shimizu, T.)

(2012) J Biol Chem 287: 40611-40617

• PubMed: 23055527 Search on PubMedSearch on PubMed Central

• DOI: https://doi.org/10.1074/jbc.M112.404608

• PubMed Abstract:
  TLR4 polymorphism replacing Asp-299 with Gly and Thr-399 with Ile (D299G/T399I) causes LPS hyporesponsiveness. TLR4(SNPs)·MD-2·LPS exhibits an agonistic 2:2:2 architecture. Local structural differences were observed around D299G, but not around T399I, SNP site. These local differences cause the modulation of surface properties of TLR4, which may affect ligand binding. This study provides structural evidence of the functionality of the mutant TLR4 carrying the SNPs. Toll-like receptor 4 (TLR4) and its coreceptor MD-2 recognize bacterial lipopolysaccharide (LPS) and signal the innate immune response. Two single nucleotide polymorphisms (SNPs) of human TLR4, D299G and T399I, have been identified and suggested to be associated with LPS hyporesponsiveness. Moreover, the SNPs have been proposed to be associated with a variety of infectious and noninfectious diseases. However, how the SNPs affect the function of TLR4 remains largely unknown. Here, we report the crystal structure of the human TLR4 (D299G/T399I)·MD-2·LPS complex at 2.4 Å resolution. The ternary complex exhibited an agonistic "m"-shaped 2:2:2 architecture that was similar to that of the human wild type TLR4·MD-2·LPS complex. Local structural differences that might affect the binding of the ligands were observed around D299G, but not around T399I, SNP site.

Organizational Affiliation:

Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Tokyo 113-0033, Japan.

Macromolecule Content

• Total Structure Weight: 184.51 kDa
• Atom Count: 12,381
• Modelled Residue Count: 1,486
• Deposited Residue Count: 1,558
• Unique protein chains: 2

Find similar proteins by:

(by identity cutoff) | 3D Structure

Find similar proteins by:

(by identity cutoff) | 3D Structure

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LP5Query on LP5Download Ideal Coordinates CCD File	M [auth C],S [auth D]	(R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATEC34 H66 N O12 PHEHQDWUWJVPREQ-XQJZMFRCSA-N		Interactions Interactions & Density
LP4Query on LP4Download Ideal Coordinates CCD File	L [auth C],R [auth D]	2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-4-O-phosphono-beta-D-glucopyranoseC34 H66 N O12 PAJRPJFBMHCTNGK-XQJZMFRCSA-N		Interactions Interactions & Density
KDOQuery on KDODownload Ideal Coordinates CCD File	P [auth C],V [auth D]	3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acidC8 H14 O8NNLZBVFSCVTSLA-HXUQBWEZSA-N		Interactions Interactions & Density
MYRQuery on MYRDownload Ideal Coordinates CCD File	O [auth C],U [auth D]	MYRISTIC ACIDC14 H28 O2TUNFSRHWOTWDNC-UHFFFAOYSA-N		Interactions Interactions & Density
NAGQuery on NAGDownload Ideal Coordinates CCD File	I [auth A],J [auth B],K [auth C],Q [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O6OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Interactions & Density
DAOQuery on DAODownload Ideal Coordinates CCD File	N [auth C],T [auth D]	LAURIC ACIDC12 H24 O2POULHZVOKOAJMA-UHFFFAOYSA-N		Interactions Interactions & Density

Experimental Data & Validation

Experimental Data

• Space Group: [C 1 2 1](/search?q=symmetry.space%5Fgroup%5Fname%5FH%5FM:C 1 2 1)

Unit Cell:

Software Package:

Revision History (Full details and data files)

• Version 1.0: 2012-10-17
  Type: Initial release
• Version 1.1: 2013-09-04
  Changes: Database references, Non-polymer description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary