Primary Citation PubMed: 19252480
Citations in PubMed
This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.
Data mentions are occurrences of PDB IDs in the full text articles from the
PubMedCentral Open Access Subset
of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed.
Article titles can be filtered by keywords and sorted by year.
Helical assembly in the MyD88-IRAK4-IRAK2 complex in TLR/IL-1R signalling.
(2010) Nature 465
PubMed: 20485341 | PubMedCentral: PMC2888693 | DOI: 10.1038/nature09121
TLRs: cyan and green (PDB code 3FXI for the extracellular domain of TLR4 and PDB code 2J67 for the TIR domain of TLR10).
MD2: yellow and magenta (PDB code 3FXI in complex TLR4).
Publication Year: 2010
Partially glycosylated dendrimers block MD-2 and prevent TLR4-MD-2-LPS complex mediated cytokine responses.
(2011) PLoS Comput Biol 7
PubMed: 21738462 | PubMedCentral: PMC3127813 | DOI: 10.1371/journal.pcbi.1002095
However, the ligand was not mouse MD-2 from the same crystal structure but instead human MD-2 from the two different crystal structures available (i.e., PDB entries: 3FXI and 2e56).
The complex of human TLR4-human MD-2 (PDB entry: 3FXI) was used as a target for the docking studies; the non-glycosylated MD-2 without ligand was extracted from the crystal structure (PDB entry: 3FXI) and loaded into Maestro.
The first studies involved the docking of the glucosamine molecules (as the moiety most likely to contribute to the biological activity of the partially glycosylated dendrimer) with the human TLR4-MD-2 complex (PDB entry: 3FXI) using Glue.
Glucosamine was docked with the human TLR4-MD-2 complex (PDB entry: 3FXI) using several overlapping target volumes defined as a box with a side of 30 Å.
Publication Year: 2011
In silico approach to inhibition of signaling pathways of Toll-like receptors 2 and 4 by ST2L.
(2011) PLoS One 6
PubMed: 21897866 | PubMedCentral: PMC3163686 | DOI: 10.1371/journal.pone.0023989
The available TLR4 ECD structure coordinates along with its ligand was taken from the PDB (3FXI).
Different dimerisation mode for TLR4 upon endosomal acidification?
(2012) Trends Biochem Sci 37
PubMed: 22196451 | PubMedCentral: PMC3323831 | DOI: 10.1016/j.tibs.2011.11.003
(a) Electrostatic surface potential in the receptor chain of the TLR4-MD-2-LPS crystal structure (PDB code 3FXI) at the dimeric interface.
The size of the dimerisation surface in the in silico -generated model (580 Å 2 ) is similar to that of the original TLR4 structure (610 Å 2 ; PDB code 3FXI) However, the participation of MD-2 in the dimerisation surface is weaker in the TLR3-derived model (77 Å 2 instead of 470 Å 2 ), and the interacting residues are different.
(a) The crystal structure of the complex formed by TLR4, MD-2 and LPS at pH 7.5 (PDB code 3FXI) forms a vertical dimer.
(d) A TLR4-MD-2-LPS dimer arranged in a TLR3-like tilted conformation was built in PyMol by superimposing receptor chain A of a first copy of 3FXI (3FXI1) onto chain A of 3CIY.
Publication Year: 2012
The lipopolysaccharide from Capnocytophaga canimorsus reveals an unexpected role of the core-oligosaccharide in MD-2 binding.
(2012) PLoS Pathog 8
PubMed: 22570611 | PubMedCentral: PMC3342949 | DOI: 10.1371/journal.ppat.1002667
Molecular modeling The MD-2 - E. coli LPS complex (PDB code 3FXI)  was used to construct models for the MD-2 - E. coli lipid A and for the MD-2 – C. canimorsus Lipid A.
Chitohexaose activates macrophages by alternate pathway through TLR4 and blocks endotoxemia.
PubMed: 22654663 | PubMedCentral: PMC3359989 | DOI: 10.1371/journal.ppat.1002717
Docking studies The X-ray structure of the extracellular domain of TLR4 (PDB code: 3FXI)  in complex with MD-2 is available.
The X-ray structure of the TLR4-MD-2 complex (3FXI) was downloaded from the PDB data base.
Mice, men and the relatives: cross-species studies underpin innate immunity.
(2012) Open Biol 2
PubMed: 22724060 | PubMedCentral: PMC3376732 | DOI: 10.1098/rsob.120015
PDB files are associated with the following references: PDB 1ziw [ 35 ]; PDB 2a0z [ 36 ]; PDBs 2z62, 2z63, 2z64, 2z65, 2z66 [ 37 ]; PDBs 2z80, 2z81, 2z82, 2z7x [ 38 ]; PDB 3ciy [ 39 ]; PDB 3fxi [ 40 ]... PDBs 3a79, 3a7b, 3a7c [ 41 ]; and PDBs 3v44, 3v47 [ 42 ].
Toll-like receptor 9 interaction with CpG ODN--an in silico analysis approach.
(2013) Theor Biol Med Model 10
PubMed: 23497207 | PubMedCentral: PMC3602074 | DOI: 10.1186/1742-4682-10-18
The final templates selected by I-TASSER were the TLR3 crystal structure (PDB code 2a0z), TLR4 crystal structure (PDB code 3fxi), TLR3 crystal structure (PDB code 1ziw), TLR4 crystal structure (PDB co... e 2z64), and TLR2 crystal structure (PDB code 2Z7X).
Publication Year: 2013
A non-synonymous coding variant (L616F) in the TLR5 gene is potentially associated with Crohn's disease and influences responses to bacterial flagellin.
(2013) PLoS One 8
PubMed: 23593463 | PubMedCentral: PMC3623901 | DOI: 10.1371/journal.pone.0061326
pdb 3 , 3FXI.
Should a Toll-like receptor 4 (TLR-4) agonist or antagonist be designed to treat cancer? TLR-4: its expression and effects in the ten most common cancers.
(2013) Onco Targets Ther 6
PubMed: 24235843 | PubMedCentral: PMC3821792 | DOI: 10.2147/OTT.S50838
The images were captured in Vida 4.2.1 (Open Eye Scientific Software, Santa Fe, NM, USA) software; using the human TLR-4/MD-2 crystal structure, with LPSEc cocrystalized (PDB ID: 3FXI).
3 TLR-4 structure Recently, TLR-4 was the first identified TLR whose crystal structure (Protein Data Bank [PDB] ID: 3FXI) was solved ( Figure 1 ), 4 leading to the derivation of computational simulation models that predict the mechanism of its interaction with its cognate ligands.
Conformationally constrained lipid A mimetics for exploration of structural basis of TLR4/MD-2 activation by lipopolysaccharide.
(2013) ACS Chem Biol 8
PubMed: 23952219 | PubMedCentral: PMC3833292 | DOI: 10.1021/cb4003199
(A) Comparison of Eritoran-hMD-2 (PDB: 2Z65) with DA193- hMD-2; (B) comparison of lipid IVa–hMD-2 (PDB: 2E59) with DA193- hMD-2; (C) comparison of Ra-LPS-hMD-2 (PDB: 3FXI) with DA193- hMD-2 (f... r clarity only Lipid A portion of LPS is shown); (D) comparison of lipid IVa-mMD-2 (PDB: 3VQ1) with DA193- mMD-2; Right: intermolecular ionic interactions of 4- and 4′- phosphates of DA193 with positively charged residues at the rim of the binding pocket of hMD-2 (E), and mMD-2 (F); ionic interactions of 4′- and 1-phosphates of lipid IVa with Lys and Arg of hMD-2 (PDB: 2E59) (G), and mMD2 (PDB: 3VQ1) (H).
Whereas all by now synthesized Lipid A analogues or Lipid A mimetics were based either on the regular β-GlcN(1→6)GlcN disaccharide backbone 27 , 28 or on the more flexible skeletons wherein the reducing GlcN was replaced by a linear aglycon, 26 , 29 we focused our research on restricting the internal flexibility of the diglucosamine backbone of Lipid A. Results and Discussion Conformational Rearrangement in Diglucosamine Backbone of Lipid A as the Key Triggering Event Required for TLR4/MD-2 Activation: Design of Trehalose-type Lipid A Mimetics Figure 3 PDB co-crystal structures of (A) hMD-2 with bound E. coli Re-LPS (PDB: 3FXI, for clarity only Lipid A portion of LPS is shown).
14 , 15 Figure 2 Side view of PDB co-crystal structures of (A) hybrid TLR4/hMD-2 with bound antagonist Eritoran (PDB: 2Z65, TLR4 is not shown); (B) hMD-2 with bound antagonist lipid IVa (PDB: 2E59); (C) mTLR4/MD-2 with bound agonist lipid IVa (PDB: 3VQ1); (D) hTLR4/MD-2 with bound E. coli Re-LPS (PDB: 3FXI, for clarity only Lipid A portion of LPS is shown).
Three-dimensional mapping of differential amino acids of human, murine, canine and equine TLR4/MD-2 receptor complexes conferring endotoxic activation by lipid A, antagonism by Eritoran and species-dependent activities of Lipid IVA in the mammalian LPS sensor system.
(2013) Comput Struct Biotechnol J 7
PubMed: 24688739 | PubMedCentral: PMC3962092 | DOI: 10.5936/csbj.201305003
Complex from Species Initial poses from PDB entry 3FXI Initial poses copied from 3FXI Initial poses with flipped backbone Initial poses from PDB entry 2E59 Initial poses copied from 2E59 Initial poses... with flipped backbone Human Lipid A - Lipid A - Lipid A Lipid A Murine - Lipid A Lipid A - Lipid A Lipid A Equine - Lipid A Lipid A - Lipid A Lipid A Human - Lipid IVA Lipid IVA Lipid IVA - Lipid IVA Murine - Lipid IVA Lipid IVA - Lipid IVA Lipid IVA Equine - Lipid IVA Lipid IVA - Lipid IVA Lipid IVA Human - Eritoran Eritoran - Eritoran Eritoran Murine - Eritoran Eritoran - Eritoran Eritoran Equine - Eritoran Eritoran - Eritoran Eritoran 36 starts = 1 + 8 + 9 + 1 + 8 + 9 We manually docked ligands into the unliganded complexes (user-attended docking) and refined interesting parts (glucosamine backbones with phosphate groups) under Autodock 4.2 (unattended docking) [ 24 , 25 , 37 ].
Figure 3 Schematic display of the rotated (′flipped′) cavity occupation in human MD-2 by acyl side chains of agonistic LPS (green) and antagonistic Lipid IVA (red), found in two crystal structures (PDB codes: 3FXI, 2E59) [ 18 , 32 ].
The 3D structures of TLR4 and MD-2 models were build as homology models using Scwrl4 [ 35 ], with the same 3D template (PDB code 3FXI [ 18 ]).
Docking of ligands into the receptor The initial ligand positions at the binding sites ( Table 1 ) were generated using as main references PDB entries 3FXI (with bound LPS), 2E59 (with bound Lipid IVA), 2Z65 (with bound Eritoran) [ 18 , 19 , 21 , 32 ].
Reviewing and identifying amino acids of human, murine, canine and equine TLR4 / MD-2 receptor complexes conferring endotoxic innate immunity activation by LPS/lipid A, or antagonistic effects by Eritoran, in contrast to species-dependent modulation by lipid IVa.
(2013) Comput Struct Biotechnol J 5
PubMed: 24688705 | PubMedCentral: PMC3962135 | DOI: 10.5936/csbj.201302012
[ 35 ] Despite the stiff appearance made by the horseshoe-like TLR4 ectomain fragments complexed with MD-2 in the LPS- or lipid IVa liganded crystal structures (PDB codes: 3FXI, 3VQ2) show a C-termina... domain rotation upon dimerization relative to the unliganded 1:1 mTLR4/MD-2 structure (PDB code: 2Z64).
As pointed out by Park and colleagues [ 8 ] the initial comparison of the human dimeric (TLR4/MD-2/Ra-LPS) 2 crystal structure (PDB code: 3FXI) with the monomeric antagonist complexes of lipid IVa with human MD-2 (PDB code: 2E59) and Eritoran with a TLR4/MD-2 fragment (PDB code: 2Z65), revealed that the presence of the two additional (secondary) acyl residues in the lipid A domain of Ra-LPS is correlated with a relative upward shift of the di-phosphorylated glucosamine backbone by approximately 5 Å towards the solvent area.
Note: our inspection of the area on crystal structure 3FXI shows that several of these amino acid residues are positioned in the TLR4 interface contacting the hydrophilic ligand backbone above the MD-2 pocket and also parts of the dimerization interface of counter-TLR4.
PDB Code Year Ref Species ( Components in complex) TITLE Resolution (Å) 2E59 Human (MD-2 / L4a) 1 2006 CRYSTAL STRUCTURE OF HUMAN MD-2 IN COMPLEX WITH LIPID IVA 2.21 [ 11 ] 2E56 Human (MD-2) 1 2006 CRYSTAL STRUCTURE OF HUMAN MD-2 2 [ 11 ] 2Z62 Human (TLR4 fragment) 1 2007 CRYSTAL STRUCTURE OF THE TV3 HYBRID OF HUMAN TLR4 AND HAGFISH VLRB.61 1.7 [ 12 ] 2Z63 Human (TLR4 fragment) 1 2007 CRYSTAL STRUCTURE OF THE TV8 HYBRID OF HUMAN TLR4 AND HAGFISH VLRB.61 2 [ 12 ] 2Z64 Mouse (TLR4 fragment / MD-2) 1 2007 CRYSTAL STRUCTURE OF MOUSE TLR4 AND MOUSE MD-2 COMPLEX 2.84 [ 9 ] 2Z65 Human (TLR4 / MD-2 / Eri) 2 2007 CRYSTAL STRUCTURE OF THE HUMAN TLR4 TV3 HYBRID-MD-2-ERITORAN COMPLEX 2.7 [ 12 ] 2Z66 Human (TLR4 fragment) 4 2007 CRYSTAL STRUCTURE OF THE VT3 HYBRID OF HUMAN TLR4 AND HAGFISH VLRB.61 1.9 [ 12 ] 3FXI Human (TLR4 / MD-2 / Ra-LPS) 2 2009 CRYSTAL STRUCTURE OF THE HUMAN TLR4-HUMAN MD-2-E.
PDB; complex with ligand L1 PDB; complex with ligand L2 L1 vs L2: Positions: above / below or equal; Effect 1: Effect 2 L1 vs L2: Orientations: fit= backbone positioning as LPS in 3FXI [ 8 ] 3VQ1; dimer: 3VQ2; dimer: L4a__LPS; fit__fit m(TLR4/MD-2/L4a) 2 m(TLR4/MD-2/LPS) 2 AG: AG 3VQ1; dimer: 2E59; monomer: L4a / L4a; fit / flipped m(TLR4/MD-2/L4a) 2 h(MD-2 /L4a) AG: AN 3FXi; dimer: 2E59; monomer: LPS / L4a; fit / flipped h(TLR4 /MD-2 /Ra-LPS) 2 h(MD-2 L4a) AG: AN 3FXi; dimer: 3VQ2; dimer: LPS __ LPS; fit __ fit h(TLR4 /MD-2 /Ra-LPS) 2 m(TLR4/MD-2/LPS) 2 AG: AG Dimerization and signaling Mechanistically different aspects of signaling are in discussion: ligand-induced oligomerization, cytoplasmically driven self-association or agonistic dimerization [ 15 , 20 , 56 ].
Identification of key residues that confer Rhodobacter sphaeroides LPS activity at horse TLR4/MD-2.
(2014) PLoS One 9
PubMed: 24879320 | PubMedCentral: PMC4039514 | DOI: 10.1371/journal.pone.0098776
The monomeric MD-2 structure extracted from 2E59 and the dimeric TLR4/MD-2 structure from 3FXI were then used in the docking experiments.
The coordinates of lipid IVa and LPS were removed from the Protein Data Bank files 2E59 and 3FXI respectively.
Publication Year: 2014
Species-specific activation of TLR4 by hypoacylated endotoxins governed by residues 82 and 122 of MD-2.
PubMed: 25203747 | PubMedCentral: PMC4159346 | DOI: 10.1371/journal.pone.0107520
 (pdb id 3FXI) and Ohto et al.
(A) Human MD-2 (pdb id 3FXI,  ) is shown in grey ribbon.
Structural insights into the human metapneumovirus glycoprotein ectodomain.
(2014) J Virol 88
PubMed: 25031352 | PubMedCentral: PMC4178817 | DOI: 10.1128/JVI.01726-14
The extracellular region of the Toll-like receptor 4–myeloid differentiation factor 2 (TLR-4/MD-2) complex (PDB identifier 3FXI ) is represented as an example of such host factor.
Development of ?GlcN(1?1)?Man-based lipid A mimetics as a novel class of potent Toll-like receptor 4 agonists.
(2014) J Med Chem 57
PubMed: 25252784 | PubMedCentral: PMC4191062 | DOI: 10.1021/jm500946r
(C) Co-crystal structure of E. coli Ra -LPS-hMD-2·TLR4 (PDB code: 3FXI; only Lipid A portion of LPS is shown for clarity), top and side views.
(B) The proximal GlcN moiety of MD-2-bound E. coli Lipid A (PDB code 3FXI) adopts inclined orientation which allows the exposure of the 2- N -acyl chain.
The location of the phosphate functionality at C-6 of the Man residue was selected to closely resemble the positioning of a 1-phosphate group of E. coli lipid A at the secondary dimerization interface of the TLR4-MD-2-Lipid A complex (PDB code 3FXI).
Insights into the species-specific TLR4 signaling mechanism in response to Rhodobacter sphaeroides lipid A detection.
(2015) Sci Rep 5
PubMed: 25563849 | PubMedCentral: PMC4288214 | DOI: 10.1038/srep07657
The control system was established by removing the ligand from the TLR4/MD2 complex crystal structure (3FXI).
Methods Homology modeling and ligand docking Human and murine X-ray crystal structures of TLR4/MD2 were retrieved from the Protein Data Bank (3FXI and 2Z64) and were used as templates to construct homology models for horse and hamster TLR4/MD2 by using MODELLER v.9.11 50 respectively.
LA containing 6 acyl chains bound to human TLR4/MD2 in an orientation where the 4′ PO 4 group was pointing at the dimer interface (3FXI).
Prefixes correspond are as follows: h (human), m (murine), e (horse), and ham (hamster) Effecter activity Complex Orientation Volume of ligand (Å 3 ) Reference Agonist hTLR4/MD2/LPS Normal 2016 3FXI Antagonist hTLR4/MD2/RsLA Flipped 1582 Modeled Antagonist hTLR4/MD2/Eritoran Flipped 1412 2Z65 Antagonist hTLR4/MD2/Lipid IVa Flipped 1393 2E59 Agonist mTLR4/MD2/LPS Normal 2016 3VQ2 Agonist mTLR4/MD2/Lipid IVa Normal 1393 3VQ1 Antagonist mTLR4/MD2/RsLA Normal 1582 Modeled Agonist eTLR4/MD2/RsLA Normal 1582 Modeled Agonist hamTLR4/MD2/RsLA Flipped 1582 Modeled Table 3 MM-PBSA values (binding free energies) of RsLA-protein complexes.
The final complexes with ligand-bound conformations were generated based on the available crystal structures of LA (3FXI) 5 , lipid IVa (2E59, 3VQ1, and 3VQ2) 24 , and Eritoran (12) (2Z65) 6 , by performing pair-wise structural alignments of the TLR4/MD2 conformations with PyMol ( www.pymol.org ).
Publication Year: 2015
PubMed ID is not available.
Published in 2015
The designs contain more than two fusion interfaces which result in large super-helical structures comparable in size to TLR4 31 (PDB ID: 3FXI, 626 residues) and plant steroid receptor BRI1 32 (PDB ID... 3RIZ, 743 residues).
(A) A ribbon representation of a TLR4/MD-2 heterodimer (pdb id 3fxi).
Protein–protein docking The crystal structures of human TLR-2-TLR-1 (2Z7X) complex, TLR-4 (3FXI) and TLR-9 (4QDH) were acquired from the Protein Data Bank.
We used the crystal structure of the LPS-liganded human TLR4/MD-2 complex (PDB code: 3FXI  ).
According to our prior studies [76,77] it has been cryptographically known that the TLR4/MD-2 complex binds reversibly a counter TLR4 (orange)/counter MD-2 (PDB code: 3FXI  ).
(A) Schematic representation of the orientation of the agonistic ligands resolved in the co-crystal structures: E. coli lipid A hMD-2·TLR4 (PDB code: 3FXI) and lipid IVa mMD-2·TLR4 (PD... code: 3VQ1) wherein the proximal (reducing) GlcN ring of the βGlcN(1↔6)GlcN backbone faces the Phe126 loop.
In contrast, the control simulation of lipid A hMD-2 revealed the Pose A (corresponding to PDB code 3FXI) as a preferred orientation in hMD-2, while pose B was disfavored by 1.6 kcal/mol, which is shown by the free energy differences between the two orientations of lipid A in the binding site of hMD-2 ( Table 2 ).
(A) Superimposition of DA193 hMD-2 (obtained by molecular dynamic simulations) and E. coli lipid A hMD-2·TLR4 (space-filling model) in the binding pocket of hMD-2 (PDB code: 3FXI).
Larger deviations are observed when hMD-2 antagonist (lipid IVa or DA193) is placed in an agonistic protein structure (3FXI).
The RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics: Rutgers and UCSD/SDSC
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.