8WRY: Mouse TLR4/MD-2/DLAM3 Complex

Cryo-EM Structure of Mouse TLR4/MD-2/DLAM3 Complex. Determined by electron microscopy at 2.6 Å resolution. Released 23 Oct 2024.

Method: Electron microscopy
Resolution: 2.6 Å
Organism: Mus musculus
Chains: 4
Atoms: 12,324
Mol. weight: 179.72 kDa
Ligands: XIQ, GP4, NAG, 0IL
Released: 23 Oct 2024

Explore 8WRY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8WRY contains 24 α-helices and 100 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: 11 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	29-32	4	18
β-strand	35-38	4	18
β-strand	57-59	3	18
β-strand	68	1	19
β-strand	81-83	3	18
β-strand	92	1	19
β-strand	105-107	3	18
β-strand	129-131	3	18
β-strand	153-155	3	18
α-helix	165-167	3
α-helix	168-172	5
β-strand	180	1	18
β-strand	188-189	2	20
α-helix	195-199	5
β-strand	216-217	2	20
β-strand	226-227	2	21
β-strand	230-231	2	22
α-helix	239-247	9
β-strand	253-254	2	21
β-strand	257-259	3	22
α-helix	273-276	4
α-helix	279-281	3
β-strand	283	1	21
β-strand	287-290	4	22
α-helix	299-301	3
β-strand	313-314	2	22
β-strand	333-336	4	22
β-strand	354-357	4	22
β-strand	364	1	23
β-strand	368	1	24
β-strand	376-377	2	22
β-strand	384	1	23
α-helix	391-393	3
β-strand	394	1	24
β-strand	409-411	3	25
β-strand	431-433	3	25
β-strand	459	1	26
β-strand	473-475	3	27
β-strand	481	1	26
α-helix	482-484	3
β-strand	485-486	2	28
β-strand	498-500	3	27
β-strand	508-509	2	28
β-strand	522-524	3	27
β-strand	533-534	2	29
β-strand	546	1	27
β-strand	557-558	2	29
β-strand	570	1	27
β-strand	571	1	30
α-helix	585-593	9
β-strand	598	1	30
α-helix	601-603	3

Chains C and D: 1 helix, 9 β-strands

Element	Residues	Length	Sheet
β-strand	23-26	4	1
β-strand	30-36	7	1
β-strand	45-49	5	2
β-strand	57-65	9	2
β-strand	74-82	9	1
β-strand	85-93	9	1
α-helix	103-106	4
β-strand	113-121	9	2
β-strand	129-139	11	1
β-strand	144-155	12	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lymphocyte antigen 96	C, D	protein	142	Mus musculus	Q9JHF9 (AlphaFold model)
Toll-like receptor 4	A, B	protein	604	Mus musculus	Q9QUK6 (AlphaFold model)

Sequence of entity 1 (C, D), FASTA

>8WRY_1 Lymphocyte antigen 96 (chains C, D)
EKQQWFCNSSDAIISYSYCDHLKFPISISSEPCIRLRGTNGFVHVEFIPRGNLKYLYFNL
FISVNSIELPKRKEVLCHGHDDDYSFCRALKGETVNTSIPFSFEGILFPKGHYRCVAEAI
AGDTEEKLFCLNFTIIHRRDVN

Sequence of entity 2 (A, B), FASTA

>8WRY_2 Toll-like receptor 4 (chains A, B)
NPCIEVVPNITYQCMDQKLSKVPDDIPSSTKNIDLSFNPLKILKSYSFSNFSELQWLDLS
RCEIETIEDKAWHGLHHLSNLILTGNPIQSFSPGSFSGLTSLENLVAVETKLASLESFPI
GQLITLKKLNVAHNFIHSCKLPAYFSNLTNLVHVDLSYNYIQTITVNDLQFLRENPQVNL
SLDMSLNPIDFIQDQAFQGIKLHELTLRGNFNSSNIMKTCLQNLAGLHVHRLILGEFKDE
RNLEIFEPSIMEGLCDVTIDEFRLTYTNDFSDDIVKFHCLANVSAMSLAGVSIKYLEDVP
KHFKWQSLSIIRCQLKQFPTLDLPFLKSLTLTMNKGSISFKKVALPSLSYLDLSRNALSF
SGCCSYSDLGTNSLRHLDLSFNGAIIMSANFMGLEELQHLDFQHSTLKRVTEFSAFLSLE
KLLYLDISYTNTKIDFDGIFLGLTSLNTLKMAGNSFKDNTLSNVFANTTNLTFLDLSKCQ
LEQISWGVFDTLHRLQLLNMSHNNLLFLDSSHYNQLYSLSTLDCSFNRIETSKGILQHFP
KSLAFFNLTNNSVACICEHQKFLQWVKEQKQFLVNVEQMTCATPVEMNTSLVLDFNNSTC
YMYK

Ligands and cofactors

ID	Name	Formula	Copies
XIQ	2-(hydroxymethyl)-5-methoxy-3,6-bis(oxidanyl)pyran-4-one	C7 H8 O6	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	16
0IL	(3R)-3-(tetradecanoyloxy)tetradecanoic acid	C28 H54 O4	2
2IL	(3R)-3-(dodecanoyloxy)tetradecanoic acid	C26 H50 O4	4

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 Q9JHF9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7MLM 2.1 Å, Crystal structure of mouse TLR4/MD-2 in complex with sulfatides
3VQ2 2.48 Å, Crystal structure of mouse TLR4/MD-2/LPS complex
5IJC 2.57 Å, The crystal structure of mouse TLR4/MD-2/neoseptin-3 complex
8WQT 2.6 Å, Cryo-EM Structure of Mouse TLR4/MD-2/DLAM1 complex
3VQ1 2.7 Å, Crystal structure of mouse TLR4/MD-2/lipid IVa complex
5IJD 2.7 Å, The crystal structure of mouse TLR4/MD-2/lipid A complex
2Z64 2.84 Å, Crystal structure of mouse TLR4 and mouse MD-2 complex
5IJB 2.91 Å, The ligand-free structure of the mouse TLR4/MD-2 complex
8WSA 3.1 Å, Cryo-EM Structure of Mouse TLR4/MD-2/DLAM5 Complex

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