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: 184.51 kDa 
• Atom Count: 12381 
• Modelled Residue Count: 1486 
• Deposited Residue Count: 1558 
• Unique protein chains: 2

4G8A

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

• DOI: 10.2210/pdb4G8A/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Drosophila
• Mutation(s): Yes 


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

---

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 

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

• PubMed: 23055527 
• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toll-like receptor 4	A, B	635	Homo sapiens	Mutation(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 GTEx:  ENSG00000136869

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lymphocyte antigen 96	C, D	144	Homo sapiens	Mutation(s): 1  Gene Names: LY96, ESOP1, MD2
Find proteins for Q9Y6Y9 (Homo sapiens) Explore Q9Y6Y9  Go to UniProtKB:  Q9Y6Y9
NIH Common Fund Data Resources
PHAROS:  Q9Y6Y9 GTEx:  ENSG00000154589

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H	2		N-Glycosylation

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LP4	C, 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
LP5	C, 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
KDO	C, D	3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid C8 H14 O8 NNLZBVFSCVTSLA-HXUQBWEZSA-N
MYR	C, D	MYRISTIC ACID C14 H28 O2 TUNFSRHWOTWDNC-UHFFFAOYSA-N
NAG	A, B, C, D	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
DAO	C, D	LAURIC ACID C12 H24 O2 POULHZVOKOAJMA-UHFFFAOYSA-N

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 = 158.038	α = 90
b = 124.68	β = 115.72
c = 109.14	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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