4G8A

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

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

Ohto, U.Yamakawa, N.Akashi-Takamura, S.Miyake, K.Shimizu, T.

(2012) J Biol Chem 287: 40611-40617

  • DOI: 10.1074/jbc.M112.404608
  • Primary Citation of Related Structures:  
    4G8A

  • PubMed Abstract: 
  • TLR4 polymorphism replacing Asp-299 with Gly and Thr-399 with Ile (D299G/T399I) causes LPS hyporesponsiveness.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Toll-like receptor 4A, B635Homo sapiensMutation(s): 2 
Gene Names: TLR4
EC: 3.2.2.6
Find proteins for O00206 (Homo sapiens)
Explore O00206 
Go to UniProtKB:  O00206
NIH Common Fund Data Resources
PHAROS:  O00206
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Lymphocyte antigen 96C, D144Homo sapiensMutation(s): 1 
Gene Names: LY96ESOP1MD2
Find proteins for Q9Y6Y9 (Homo sapiens)
Explore Q9Y6Y9 
Go to UniProtKB:  Q9Y6Y9
NIH Common Fund Data Resources
PHAROS:  Q9Y6Y9
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE, F, G, H2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LP4
Query on LP4

Download 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-glucopyranose
C34 H66 N O12 P
AJRPJFBMHCTNGK-XQJZMFRCSA-N
 Ligand Interaction
LP5
Query on LP5

Download 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-HYDROXYTETRADECANOATE
C34 H66 N O12 P
HEHQDWUWJVPREQ-XQJZMFRCSA-N
 Ligand Interaction
KDO
Query on KDO

Download Ideal Coordinates CCD File 
P [auth C], V [auth D]3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid
C8 H14 O8
NNLZBVFSCVTSLA-HXUQBWEZSA-N
 Ligand Interaction
MYR
Query on MYR

Download Ideal Coordinates CCD File 
O [auth C], U [auth D]MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
I [auth A], J [auth B], K [auth C], Q [auth D]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
DAO
Query on DAO

Download Ideal Coordinates CCD File 
N [auth C], T [auth D]LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.038α = 90
b = 124.68β = 115.72
c = 109.14γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2012-07-23 
  • Released Date: 2012-10-17 
  • Deposition Author(s): Ohto, U., Shimizu, T.

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