5IJD: Mouse TLR4/MD-2/lipid A complex

The crystal structure of mouse TLR4/MD-2/lipid A complex. Determined by X-ray diffraction at 2.7 Å resolution. Released 27 Apr 2016.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Mus musculus, Eptatretus burgeri
Chains: 4
Atoms: 12,385
Mol. weight: 177.13 kDa
Ligands: MYR, DAO, LP5, LP4
Released: 27 Apr 2016

Explore 5IJD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5IJD contains 31 α-helices and 108 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: 12 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	30-32	3	1
β-strand	36-38	3	1
β-strand	57-59	3	1
β-strand	67-68	2	2
β-strand	81-83	3	1
β-strand	91-92	2	2
β-strand	105-107	3	1
β-strand	129-131	3	1
β-strand	153-155	3	1
α-helix	169-171	3
β-strand	178-180	3	1
β-strand	188-189	2	3
α-helix	195-198	4
β-strand	207-208	2	1
β-strand	216-217	2	3
β-strand	226-233	8	1
α-helix	239-247	9
β-strand	253-260	8	1
α-helix	273-276	4
β-strand	283-289	7	1
α-helix	297-301	5
α-helix	303-305	3
β-strand	310-314	5	1
β-strand	332-336	5	1
α-helix	343-345	3
β-strand	353-357	5	1
β-strand	364	1	4
β-strand	375-377	3	1
β-strand	384	1	4
β-strand	385-388	4	5
α-helix	391-394	4
β-strand	401-403	3	1
β-strand	409-412	4	5
β-strand	424-426	3	1
β-strand	431-433	3	5
β-strand	449-451	3	1
β-strand	458-459	2	6
α-helix	462-465	4
β-strand	473-475	3	1
β-strand	480-481	2	6
α-helix	482-484	3
β-strand	485-486	2	7
β-strand	498-500	3	1
β-strand	508-509	2	7
β-strand	522-524	3	1
β-strand	546-548	3	1
β-strand	570-572	3	1
β-strand	578	1	8
α-helix	586-594	9
β-strand	599-600	2	1
β-strand	604	1	9
β-strand	605	1	8
β-strand	611	1	9
α-helix	612-614	3

Chain B: 9 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	32	1	16
β-strand	36	1	16
β-strand	57-59	3	16
β-strand	67	1	17
β-strand	81-83	3	16
β-strand	91	1	17
β-strand	105-107	3	16
β-strand	129-131	3	16
β-strand	153-155	3	16
α-helix	168-171	4
β-strand	178-180	3	16
β-strand	188-189	2	18
β-strand	205-208	4	16
β-strand	216-217	2	18
β-strand	226-233	8	16
α-helix	239-247	9
β-strand	253-260	8	16
α-helix	273-276	4
β-strand	283-289	7	16
α-helix	298-301	4
α-helix	303-305	3
β-strand	311-314	4	16
β-strand	332-336	5	16
α-helix	343-345	3
β-strand	353-357	5	16
β-strand	364	1	19
β-strand	375-377	3	16
β-strand	384	1	19
β-strand	385-388	4	20
α-helix	391-394	4
β-strand	401-403	3	16
β-strand	409-412	4	20
β-strand	424-426	3	16
β-strand	431-433	3	20
β-strand	449-451	3	16
β-strand	458-459	2	21
β-strand	473-475	3	16
β-strand	480-481	2	21
α-helix	482-484	3
β-strand	485-486	2	22
β-strand	498-500	3	16
β-strand	508-509	2	22
β-strand	522-524	3	16
β-strand	546-548	3	16
β-strand	570-572	3	16
β-strand	578	1	23
α-helix	586-595	10
β-strand	599-600	2	16
β-strand	604	1	24
β-strand	605	1	23
β-strand	611	1	24

Chain C: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	23-26	4	10
β-strand	30-36	7	10
β-strand	37	1	11
β-strand	40	1	11
β-strand	44-49	6	12
α-helix	51-53	3
β-strand	56-65	10	12
β-strand	74-82	9	10
β-strand	85-86	2	10
α-helix	87-88	2
β-strand	90-93	4	10
α-helix	103-106	4
β-strand	113-122	10	12
α-helix	123-125	3
β-strand	129-139	11	10
β-strand	144-155	12	10

Chain D: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	21-26	6	13
β-strand	30-36	7	13
β-strand	37	1	14
β-strand	40	1	14
β-strand	45-47	3	15
α-helix	51-53	3
β-strand	56-65	10	15
β-strand	74-82	9	13
β-strand	85-86	2	13
α-helix	87-88	2
β-strand	90-93	4	13
α-helix	103-106	4
α-helix	107-108	2
β-strand	113-122	10	15
α-helix	123-124	2
α-helix	126-127	2
β-strand	129-139	11	13
β-strand	144-155	12	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Toll-like receptor 4, Variable lymphocyte receptor B chimera	A, B	protein	594	Mus musculus, Eptatretus burgeri	Q4G1L2 (AlphaFold model), Q9QUK6 (AlphaFold model)
Lymphocyte antigen 96	C, D	protein	150	Mus musculus	Q9JHF9 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5IJD_1 Toll-like receptor 4, Variable lymphocyte receptor B chimera (chains A, B)
NPCIEVVPNITYQCMDQKLSKVPDDIPSSTKNIDLSFNPLKILKSYSFSNFSELQWLDLS
RCEIETIEDKAWHGLHHLSNLILTGNPIQSFSPGSFSGLTSLENLVAVETKLASLESFPI
GQLITLKKLNVAHNFIHSCKLPAYFSNLTNLVHVDLSYNYIQTITVNDLQFLRENPQVNL
SLDMSLNPIDFIQDQAFQGIKLHELTLRGNFNSSNIMKTCLQNLAGLHVHRLILGEFKDE
RNLEIFEPSIMEGLCDVTIDEFRLTYTNDFSDDIVKFHCLANVSAMSLAGVSIKYLEDVP
KHFKWQSLSIIRCQLKQFPTLDLPFLKSLTLTMNKGSISFKKVALPSLSYLDLSRNALSF
SGCCSYSDLGTNSLRHLDLSFNGAIIMSANFMGLEELQHLDFQHSTLKRVTEFSAFLSLE
KLLYLDISYTNTKIDFDGIFLGLTSLNTLKMAGNSFKDNTLSNVFANTTNLTFLDLSKCQ
LEQISWGVFDTLHRLQLLNMSHNNLLFLDSSHYNQLYSLKELALDTNQLKSVPDGIFDRL
TSLQKIWLHTNPWDCSCPRIDYLSRWLNKNSQKEQGSAKCSGSGKPVRSIICPT

Sequence of entity 2 (C, D), FASTA

>5IJD_2 Lymphocyte antigen 96 (chains C, D)
EKQQWFCNSSDAIISYSYCDHLKFPISISSEPCIRLRGTNGFVHVEFIPRGNLKYLYFNL
FISVNSIELPKRKEVLCHGHDDDYSFCRALKGETVNTSIPFSFEGILFPKGHYRCVAEAI
AGDTEEKLFCLNFTIIHRRDVNKGENLYFQ

Ligands and cofactors

ID	Name	Formula	Copies
MYR	Myristic acid	C14 H28 O2	2
DAO	Lauric acid	C12 H24 O2	2
LP5	(r)-((2R,3S,4R,5R,6R)-3-hydroxy-2-(hydroxymethyl)-5-((R)-3-hydroxytetradecanami…	C34 H66 N O12 P	2
LP4	2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino…	C34 H66 N O12 P	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

Primary citation

TLR4/MD-2 activation by a synthetic agonist with no similarity to LPS. Wang, Y., Su, L., Morin, M.D. et al. Proc Natl Acad Sci U S A (2016) 113:E884-E893. DOI 10.1073/pnas.1525639113 · PubMed

Other PDB entries of the same protein (UniProt Q4G1L2 (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
5GY2 2.1 Å, Crystal structure of a complex between Bacillus subtilis flagellin and zebrafish…
7MLM 2.1 Å, Crystal structure of mouse TLR4/MD-2 in complex with sulfatides
4QXE 2.2 Å, Crystal structure of LGR4 fused with hagfish VLR
4QXF 2.25 Å, crystal structure of human LGR4 and Rspo1
6BXA 2.3 Å, Crystal structure of N-terminal fragment of Zebrafish Toll-Like Receptor 5 (TLR5) with…
2O6R 2.3 Å, Structural diversity of the hagfish Variable Lymphocyte Receptors B61
4BV4 2.35 Å, Structure and allostery in Toll-Spatzle recognition
3UL7 2.37 Å, Crystal structure of the TV3 mutant F63W
4QDH 2.4 Å, Crystal Structure of the C-terminal Domain of Mouse TLR9

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