3VQ1: Mouse TLR4/MD-2/lipid IVa complex

Crystal structure of mouse TLR4/MD-2/lipid IVa complex. Determined by X-ray diffraction at 2.7 Å resolution. Released 9 May 2012.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Mus musculus
Chains: 4
Atoms: 12,017
Mol. weight: 175.25 kDa
Ligands: LP4, LP5, NAG
Released: 9 May 2012

Explore 3VQ1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3VQ1 contains 33 α-helices and 106 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: 14 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	29-32	4	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	168-171	4
β-strand	178-180	3	1
β-strand	188-189	2	3
α-helix	195-199	5
β-strand	206-208	3	1
β-strand	216-217	2	3
β-strand	226-233	8	1
α-helix	239-246	8
α-helix	247-249	3
β-strand	253-260	8	1
β-strand	262	1	4
β-strand	265	1	4
α-helix	273-280	8
β-strand	283-289	7	1
α-helix	297-299	3
α-helix	303-305	3
β-strand	310-314	5	1
β-strand	332-336	5	1
β-strand	353-357	5	1
β-strand	364	1	5
β-strand	375-377	3	1
β-strand	384	1	5
β-strand	385-388	4	6
α-helix	391-394	4
β-strand	401-403	3	1
β-strand	409-412	4	6
β-strand	424-426	3	1
β-strand	431-433	3	6
β-strand	449-451	3	1
β-strand	458-459	2	7
β-strand	473-475	3	1
β-strand	480-481	2	7
α-helix	482-484	3
β-strand	485-486	2	8
β-strand	498-500	3	1
β-strand	508-509	2	8
β-strand	522-524	3	1
β-strand	533-534	2	9
α-helix	535-537	3
β-strand	546-548	3	1
β-strand	557-558	2	9
α-helix	561-563	3
β-strand	570-572	3	1
α-helix	582-584	3
α-helix	585-593	9
β-strand	598-599	2	1
α-helix	601-603	3

Chain B: 13 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	29-32	4	13
β-strand	36-38	3	13
β-strand	57-59	3	13
β-strand	67-68	2	14
β-strand	73	1	15
β-strand	81-83	3	13
β-strand	91-92	2	14
β-strand	97	1	15
β-strand	105-107	3	13
β-strand	129-131	3	13
β-strand	153-155	3	13
α-helix	168-171	4
β-strand	178-180	3	13
β-strand	188-189	2	16
α-helix	195-198	4
β-strand	206-208	3	13
β-strand	216-217	2	16
β-strand	225-233	9	13
α-helix	239-247	9
β-strand	252-260	9	13
α-helix	273-281	9
β-strand	283-289	7	13
α-helix	297-299	3
α-helix	303-305	3
β-strand	310-314	5	13
β-strand	332-336	5	13
α-helix	343-345	3
β-strand	353-357	5	13
β-strand	364	1	17
β-strand	375-377	3	13
β-strand	384	1	17
β-strand	385-388	4	18
α-helix	391-394	4
β-strand	401-403	3	13
β-strand	409-412	4	18
β-strand	424-426	3	13
β-strand	431-433	3	18
β-strand	449-451	3	13
β-strand	458-459	2	19
β-strand	473-475	3	13
β-strand	480-481	2	19
α-helix	482-484	3
β-strand	485-486	2	20
β-strand	498-500	3	13
β-strand	508-509	2	20
β-strand	522-524	3	13
β-strand	533-534	2	21
α-helix	535-538	4
β-strand	546-548	3	13
β-strand	557-558	2	21
α-helix	561-563	3
β-strand	570-572	3	13
α-helix	582-584	3
α-helix	585-593	9
β-strand	598	1	13

Chain C: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	23-27	5	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	57-65	9	12
β-strand	74-82	9	10
β-strand	85-86	2	10
α-helix	87-89	3
β-strand	90-93	4	10
α-helix	103-106	4
α-helix	107-108	2
β-strand	113-121	9	12
β-strand	130-139	10	10
β-strand	144-154	11	10

Chain D: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	23-27	5	22
β-strand	30-36	7	22
β-strand	44-49	6	23
α-helix	51-53	3
β-strand	57-65	9	23
β-strand	74-82	9	22
β-strand	85-86	2	22
β-strand	90-93	4	22
α-helix	103-106	4
β-strand	113-121	9	23
β-strand	130-139	10	22
β-strand	144-154	11	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Toll-like receptor 4	A, B	protein	606	Mus musculus	Q9QUK6 (AlphaFold model)
Lymphocyte antigen 96	C, D	protein	144	Mus musculus	Q9JHF9 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3VQ1_1 Toll-like receptor 4 (chains A, B)
PGSLNPCIEVVPNITYQCMDQKLSKVPDDIPSSTKNIDLSFNPLKILKSYSFSNFSELQW
LDLSRCEIETIEDKAWHGLHHLSNLILTGNPIQSFSPGSFSGLTSLENLVAVETKLASLE
SFPIGQLITLKKLNVAHNFIHSCKLPAYFSNLTNLVHVDLSYNYIQTITVNDLQFLRENP
QVNLSLDMSLNPIDFIQDQAFQGIKLHELTLRGNFNSSNIMKTCLQNLAGLHVHRLILGE
FKDERNLEIFEPSIMEGLCDVTIDEFRLTYTNDFSDDIVKFHCLANVSAMSLAGVSIKYL
EDVPKHFKWQSLSIIRCQLKQFPTLDLPFLKSLTLTMNKGSISFKKVALPSLSYLDLSRN
ALSFSGCCSYSDLGTNSLRHLDLSFNGAIIMSANFMGLEELQHLDFQHSTLKRVTEFSAF
LSLEKLLYLDISYTNTKIDFDGIFLGLTSLNTLKMAGNSFKDNTLSNVFANTTNLTFLDL
SKCQLEQISWGVFDTLHRLQLLNMSHNNLLFLDSSHYNQLYSLSTLDCSFNRIETSKGIL
QHFPKSLAFFNLTNNSVACICEHQKFLQWVKEQKQFLVNVEQMTCATPVEMNTSLVLDFN
NSTCYM

Sequence of entity 2 (C, D), FASTA

>3VQ1_2 Lymphocyte antigen 96 (chains C, D)
ESEKQQWFCNSSDAIISYSYCDHLKFPISISSEPCIRLRGTNGFVHVEFIPRGNLKYLYF
NLFISVNSIELPKRKEVLCHGHDDDYSFCRALKGETVNTSIPFSFEGILFPKGHYRCVAE
AIAGDTEEKLFCLNFTIIHRRDVN

Ligands and cofactors

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

Primary citation

Structural basis of species-specific endotoxin sensing by innate immune receptor TLR4/MD-2. Ohto, U., Fukase, K., Miyake, K. et al. Proc Natl Acad Sci U S A (2012) 109:7421-7426. DOI 10.1073/pnas.1201193109 · PubMed

Other PDB entries of the same protein (UniProt Q9QUK6 (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
8WRY 2.6 Å, Cryo-EM Structure of Mouse TLR4/MD-2/DLAM3 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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