9J03: Lymphocyte antigen 96

Cyro-EM Structure of Human TLR4/MD-2/DLAM1 Complex. Determined by electron microscopy at 2.7 Å resolution. Released 14 May 2025.

Method: Electron microscopy
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 4
Atoms: 12,412
Mol. weight: 178.68 kDa
Ligands: X6Z, GP4, NAG, 2IL
Released: 14 May 2025

Explore 9J03 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9J03 contains 20 α-helices and 116 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.

Chains A and B: 7 helices, 49 β-strands

Element	Residues	Length	Sheet
β-strand	30-33	4	20
β-strand	37-41	5	20
β-strand	59-62	4	20
β-strand	69	1	21
β-strand	79	1	22
β-strand	82-84	3	20
β-strand	92-93	2	21
β-strand	102	1	22
β-strand	106-108	3	20
β-strand	116-117	2	21
β-strand	130-132	3	20
β-strand	156	1	20
α-helix	169-172	4
β-strand	179-181	3	20
β-strand	189-190	2	23
β-strand	207-209	3	20
β-strand	217-218	2	23
β-strand	230	1	20
β-strand	231-234	4	24
α-helix	240-249	10
β-strand	258-261	4	24
α-helix	280-282	3
β-strand	287	1	25
β-strand	288-290	3	24
β-strand	293	1	26
β-strand	312	1	25
β-strand	315-316	2	24
β-strand	318	1	26
β-strand	331	1	27
β-strand	337-338	2	24
β-strand	349	1	28
β-strand	352	1	27
β-strand	371	1	28
β-strand	379	1	29
β-strand	387	1	30
α-helix	393-396	4
β-strand	405	1	29
β-strand	412-413	2	30
β-strand	428	1	29
β-strand	434-435	2	30
β-strand	451-453	3	29
β-strand	460-461	2	31
β-strand	475-477	3	29
β-strand	482-483	2	31
α-helix	484-486	3
β-strand	487-488	2	32
β-strand	500-502	3	29
β-strand	510-511	2	32
β-strand	524-525	2	29
β-strand	526	1	33
β-strand	534-535	2	34
β-strand	548-550	3	33
β-strand	558-559	2	34
α-helix	566-568	3
β-strand	573-575	3	33
α-helix	588-594	7

Chains C and D: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	22-27	6	1
β-strand	30-36	7	1
β-strand	45-49	5	2
α-helix	51-53	3
β-strand	57-65	9	2
β-strand	75-82	8	1
β-strand	86-93	8	1
α-helix	104-106	3
α-helix	111-112	2
β-strand	113-121	9	2
β-strand	131-139	9	1
β-strand	144-153	10	1

Molecules and chains

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

Sequence of entity 1 (C, D), FASTA

>9J03_1 Lymphocyte antigen 96 (chains C, D)
QKQYWVCNSSDASISYTYCDKMQYPISINVNPCIELKGSKGLLHIFYIPRRDLKQLYFNL
YITVNTMNLPKRKEVICRGSDDDYSFCRALKGETVNTTISFSFKGIKFSKGKYKCVVEAI
SGSPEEMLFCLEFVILHQPNSN

Sequence of entity 2 (A, B), FASTA

>9J03_2 Toll-like receptor 4 (chains A, B)
EPCVEVVPNITYQCMELNFYKIPDNLPFSTKNLDLSFNPLRHLGSYSFFSFPELQVLDLS
RCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQKLVAVETNLASLENFPI
GHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQMPLLNL
SLDLSLNPMNFIQPGAFKEIRLHKLTLRNNFDSLNVMKTCIQGLAGLEVHRLVLGEFRNE
GNLEKFDKSALEGLCNLTIEEFRLAYLDYYLDDIIDLFNCLTNVSSFSLVSVTIERVKDF
SYNFGWQHLELVNCKFGQFPTLKLKSLKRLTFTSNKGGNAFSEVDLPSLEFLDLSRNGLS
FKGCCSQSDFGTTSLKYLDLSFNGVITMSSNFLGLEQLEHLDFQHSNLKQMSEFSVFLSL
RNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQC
QLEQLSPTAFNSLSSLQVLNMSHNNFFSLDTFPYKCLNSLQVLDYSLNHIMTSKKQELQH
FPSSLAFLNLTQNDFACTCEHQSFLQWIKDQRQLLVEVERMECATPSDKQGMPVLSLNIT
CQMNK

Ligands and cofactors

ID	Name	Formula	Copies
X6Z	[(2~{R},3~{S},4~{S},5~{S})-5-methoxy-3,4,6-tris(oxidanyl)oxan-2-yl]methyl…	C7 H15 O9 P	2
GP4	2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose	C6 H14 N O8 P	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6
2IL	(3R)-3-(dodecanoyloxy)tetradecanoic acid	C26 H50 O4	6

Primary citation

Structural insight into TLR4/MD-2 activation by synthetic LPS mimetics with distinct binding modes. Fu, Y., Kim, H., Lee, D.S. et al. Nat Commun (2025) 16:4164-4164. DOI 10.1038/s41467-025-59550-3 · PubMed

Other PDB entries of the same protein (UniProt Q9Y6Y9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2E56 2.0 Å, Crystal structure of human MD-2
2E59 2.21 Å, Crystal structure of human MD-2 in complex with lipid IVa
8WO1 2.24 Å, Cryo-EM Structure of Human TLR4/MD-2/DLAM5 Complex
4G8A 2.4 Å, Crystal structure of human TLR4 polymorphic variant D299G and T399I in complex with MD-2…
2Z65 2.7 Å, Crystal structure of the human TLR4 TV3 hybrid-MD-2-Eritoran complex
8WTA 2.9 Å, Cryo-EM Structure of Human TLR4/MD-2/DLAM3 Complex
3FXI 3.1 Å, Crystal structure of the human TLR4-human MD-2-E.coli LPS Ra complex
3ULA 3.6 Å, Crystal structure of the TV3 mutant F63W-MD-2-Eritoran complex

Browse structure collections

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