9J03 | pdb_00009j03

Cyro-EM Structure of Human TLR4/MD-2/DLAM1 Complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9J03

This is version 1.0 of the entry. See complete history

Literature

Structural insight into TLR4/MD-2 activation by synthetic LPS mimetics with distinct binding modes.

Fu, Y.Kim, H.Lee, D.S.Han, A.R.Heine, H.Zamyatina, A.Kim, H.M.

(2025) Nat Commun 16: 4164-4164

  • DOI: https://doi.org/10.1038/s41467-025-59550-3
  • Primary Citation Related Structures: 
    8WO1, 8WQT, 8WRY, 8WSA, 8WTA, 9J03

  • PubMed Abstract: 

    The mammalian pattern-recognition receptor TLR4/MD-2 (Toll-like receptor 4/myeloid differentiation factor-2) can be activated by a wide variety of pathogen-associated and endogenous molecules, with Gram-negative bacterial lipopolysaccharide (LPS) being the primary natural TLR4 agonist. Activation of TLR4 triggers cellular signaling that enables the beneficial innate immune responses and enhances adaptive immunity, thereby emphasizing the potential of TLR4 agonists for the management of diseases with an immunopathological background and for use as vaccine adjuvants. Given the challenges associated with LPS-derived products, including structural complexity, heterogeneity, toxicity, and species specificity, synthetic molecules targeting TLR4/MD-2 offer a promising alternative. Here, we elucidate the structural basis for the recognition of synthetic LPS-mimicking glycolipids, Disaccharide Lipid A Mimetics (DLAMs), by human and mouse TLR4/MD-2 through cryo-EM structures of six dimeric [TLR4/MD-2/ligand] 2 complexes resolved at 2.2-3.1 Å. We reveal that the specific binding modes of DLAMs, distinct from those of LPS, are essential for the species-independent TLR4 agonistic activity. DLAMs function as a molecular bridge, effectively induce the dimerization of TLR4/MD-2 complexes through specific carbohydrate structure-relevant ligand-protein interactions. Our findings reveal the distinct molecular modes of TLR4 activation, and provide a structural basis for the rationale design and development of innovative, highly potent TLR4-targeting immunotherapeutics and adjuvants.


  • Organizational Affiliation
    • Department of Biological Science, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 178.68 kDa 
  • Atom Count: 12,412 
  • Modeled Residue Count: 1,482 
  • Deposited Residue Count: 1,494 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lymphocyte antigen 96A [auth C],
B [auth D]
142Homo sapiensMutation(s): 0 
Gene Names: LY96
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
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q9Y6Y9-1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Toll-like receptor 4C [auth B],
D [auth A]
605Homo sapiensMutation(s): 0 
Gene Names: TLR4
UniProt & NIH Common Fund Data Resources
Find proteins for O00206 (Homo sapiens)
Explore O00206 
Go to UniProtKB:  O00206
PHAROS:  O00206
GTEx:  ENSG00000136869 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00206
Glycosylation
Glycosylation Sites: 4Go to GlyGen: O00206-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 4
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-glucopyranoseG,
H [auth I]
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseI [auth P],
J [auth H]
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G47362BJ
GlyCosmos: G47362BJ
GlyGen: G47362BJ

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2IL
(Subject of Investigation/LOI)

Query on 2IL



Download:Ideal Coordinates CCD File
K [auth C]
L [auth C]
M [auth C]
P [auth D]
Q [auth D]
K [auth C],
L [auth C],
M [auth C],
P [auth D],
Q [auth D],
X [auth A]
(3R)-3-(dodecanoyloxy)tetradecanoic acid
C26 H50 O4
IKRFTYQBIVDIMM-XMMPIXPASA-N
X6Z
(Subject of Investigation/LOI)

Query on X6Z



Download:Ideal Coordinates CCD File
S [auth B],
W [auth A]
[(2~{R},3~{S},4~{S},5~{S})-5-methoxy-3,4,6-tris(oxidanyl)oxan-2-yl]methyl dihydrogen phosphate
C7 H15 O9 P
KJZYYYMWKHTJAM-VEIUFWFVSA-N
GP4
(Subject of Investigation/LOI)

Query on GP4



Download:Ideal Coordinates CCD File
R [auth B],
V [auth A]
2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose
C6 H14 N O8 P
QWDBGVNDGYUIAC-UKFBFLRUSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
N [auth C]
O [auth D]
T [auth B]
U [auth B]
Y [auth A]
N [auth C],
O [auth D],
T [auth B],
U [auth B],
Y [auth A],
Z [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-14
    Type: Initial release