3FXI: Human TLR4-human MD-2-E.coli LPS Ra complex

Crystal structure of the human TLR4-human MD-2-E.coli LPS Ra complex. Determined by X-ray diffraction at 3.1 Å resolution. Released 3 Mar 2009.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 12,500
Mol. weight: 180.25 kDa
Ligands: PO4, MYR, DAO, FTT
Released: 3 Mar 2009

Explore 3FXI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3FXI contains 35 α-helices and 105 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 15 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	30-33	4	1
β-strand	37-39	3	1
β-strand	58-60	3	1
β-strand	69	1	2
β-strand	82-84	3	1
β-strand	92-93	2	2
β-strand	106-108	3	1
β-strand	116-117	2	2
β-strand	130-132	3	1
β-strand	154-156	3	1
α-helix	169-171	3
β-strand	179-181	3	1
β-strand	189-190	2	3
α-helix	192-195	4
α-helix	198-200	3
β-strand	207-209	3	1
β-strand	217-218	2	3
β-strand	227-234	8	1
α-helix	240-249	10
β-strand	254-261	8	1
α-helix	267-269	3
α-helix	278-282	5
β-strand	284-293	10	1
α-helix	305-307	3
β-strand	312-318	7	1
β-strand	319	1	4
β-strand	334-338	5	1
β-strand	341	1	4
α-helix	345-346	2
β-strand	355-359	5	1
β-strand	362	1	4
β-strand	366	1	5
β-strand	377-379	3	1
β-strand	386	1	5
β-strand	387-392	6	6
α-helix	393-396	4
β-strand	403-405	3	1
β-strand	411-419	9	6
β-strand	426-428	3	1
β-strand	433-435	3	6
β-strand	438	1	7
β-strand	440-441	2	7
β-strand	451-453	3	1
β-strand	461	1	8
β-strand	477	1	1
β-strand	483	1	8
α-helix	484-486	3
β-strand	502	1	1
α-helix	516-518	3
β-strand	526	1	1
α-helix	539-542	4
α-helix	585-587	3
α-helix	588-596	9
α-helix	604-606	3
β-strand	608	1	9
β-strand	619	1	9

Chain B: 14 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	30-33	4	10
β-strand	37-39	3	10
β-strand	58-60	3	10
β-strand	69	1	11
β-strand	82-84	3	10
β-strand	92-93	2	11
β-strand	106-108	3	10
β-strand	116-117	2	11
β-strand	130-132	3	10
β-strand	154-156	3	10
α-helix	169-172	4
β-strand	179-181	3	10
β-strand	189-190	2	12
α-helix	192-195	4
α-helix	198-200	3
β-strand	207-209	3	10
β-strand	217-218	2	12
β-strand	227-234	8	10
α-helix	240-249	10
β-strand	254-261	8	10
α-helix	267-269	3
α-helix	278-282	5
β-strand	284-293	10	10
α-helix	305-307	3
β-strand	312-318	7	10
β-strand	334-338	5	10
β-strand	341	1	13
α-helix	345-346	2
β-strand	355-359	5	10
β-strand	362	1	13
β-strand	366	1	14
β-strand	377-379	3	10
β-strand	386	1	14
β-strand	387-392	6	15
β-strand	403-405	3	10
β-strand	411-419	9	15
β-strand	426-428	3	10
β-strand	433-435	3	15
β-strand	438	1	16
β-strand	440-441	2	16
β-strand	451-453	3	10
β-strand	461	1	17
β-strand	477	1	10
β-strand	483	1	17
α-helix	484-486	3
β-strand	502	1	10
α-helix	516-518	3
β-strand	526	1	10
α-helix	539-542	4
α-helix	585-587	3
α-helix	588-596	9
α-helix	604-606	3
β-strand	608	1	18
β-strand	619	1	18

Chains C and D: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	20-21	2
β-strand	22-26	5	19
β-strand	30-36	7	19
β-strand	45-49	5	20
β-strand	57	1	21
β-strand	60-65	6	20
β-strand	75-82	8	19
β-strand	85-86	2	19
α-helix	87-89	3
β-strand	90-93	4	19
α-helix	103-106	4
β-strand	113-118	6	20
β-strand	121	1	21
β-strand	129-139	11	19
β-strand	144-155	12	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Toll-like receptor 4	A, B	protein	605	Homo sapiens	O00206 (AlphaFold model)
Lymphocyte antigen 96	C, D	protein	142	Homo sapiens	Q9Y6Y9 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3FXI_1 Toll-like receptor 4 (chains A, B)
EPCVEVVPNITYQCMELNFYKIPDNLPFSTKNLDLSFNPLRHLGSYSFFSFPELQVLDLS
RCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQKLVAVETNLASLENFPI
GHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQMPLLNL
SLDLSLNPMNFIQPGAFKEIRLHKLTLRNNFDSLNVMKTCIQGLAGLEVHRLVLGEFRNE
GNLEKFDKSALEGLCNLTIEEFRLAYLDYYLDDIIDLFNCLTNVSSFSLVSVTIERVKDF
SYNFGWQHLELVNCKFGQFPTLKLKSLKRLTFTSNKGGNAFSEVDLPSLEFLDLSRNGLS
FKGCCSQSDFGTTSLKYLDLSFNGVITMSSNFLGLEQLEHLDFQHSNLKQMSEFSVFLSL
RNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQC
QLEQLSPTAFNSLSSLQVLNMSHNNFFSLDTFPYKCLNSLQVLDYSLNHIMTSKKQELQH
FPSSLAFLNLTQNDFACTCEHQSFLQWIKDQRQLLVEVERMECATPSDKQGMPVLSLNIT
CQMNK

Sequence of entity 2 (C, D), FASTA

>3FXI_2 Lymphocyte antigen 96 (chains C, D)
QKQYWVCNSSDASISYTYCDKMQYPISINVNPCIELKGSKGLLHIFYIPRRDLKQLYFNL
YITVNTMNLPKRKEVICRGSDDDYSFCRALKGETVNTTISFSFKGIKFSKGKYKCVVEAI
SGSPEEMLFCLEFVILHQPNSN

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	8
MYR	Myristic acid	C14 H28 O2	2
DAO	Lauric acid	C12 H24 O2	2
FTT	3-hydroxy-tetradecanoic acid	C14 H28 O3	8
MG	Magnesium ion	Mg	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	8

Primary citation

The structural basis of lipopolysaccharide recognition by the TLR4-MD-2 complex. Park, B.S., Song, D.H., Kim, H.M. et al. Nature (2009) 458:1191-1195. DOI 10.1038/nature07830 · PubMed

Other PDB entries of the same protein (UniProt O00206 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2Z62 1.7 Å, Crystal structure of the TV3 hybrid of human TLR4 and hagfish VLRB.61
2Z66 1.9 Å, Crystal structure of the VT3 hybrid of human TLR4 and hagfish VLRB.61
2Z63 2.0 Å, Crystal structure of the TV8 hybrid of human TLR4 and hagfish VLRB.61
8WO1 2.24 Å, Cryo-EM Structure of Human TLR4/MD-2/DLAM5 Complex
3UL7 2.37 Å, Crystal structure of the TV3 mutant F63W
4G8A 2.4 Å, Crystal structure of human TLR4 polymorphic variant D299G and T399I in complex with MD-2…
3UL9 2.45 Å, structure of the TV3 mutant M41E
3UL8 2.5 Å, Crystal structure of the TV3 mutant V134L
2Z65 2.7 Å, Crystal structure of the human TLR4 TV3 hybrid-MD-2-Eritoran complex
9J03 2.7 Å, Cyro-EM Structure of Human TLR4/MD-2/DLAM1 Complex
8WTA 2.9 Å, Cryo-EM Structure of Human TLR4/MD-2/DLAM3 Complex
3ULA 3.6 Å, Crystal structure of the TV3 mutant F63W-MD-2-Eritoran complex

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