4G8A: Human TLR4 polymorphic variant D299G and T399I

Crystal structure of human TLR4 polymorphic variant D299G and T399I in complex with MD-2 and LPS. Determined by X-ray diffraction at 2.4 Å resolution. Released 17 Oct 2012.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 4
Atoms: 12,381
Mol. weight: 184.51 kDa
Ligands: NAG, LP4, LP5, DAO
Released: 17 Oct 2012

Explore 4G8A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4G8A contains 36 α-helices and 121 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: 16 helices, 50 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	68-69	2	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
α-helix	119-122	4
β-strand	130-132	3	1
β-strand	154-156	3	1
α-helix	166-168	3
α-helix	169-173	5
β-strand	179-181	3	1
β-strand	189-190	2	3
α-helix	192-195	4
α-helix	196-199	4
β-strand	207-209	3	1
β-strand	217-218	2	3
β-strand	227-234	8	1
α-helix	240-248	9
β-strand	254-261	8	1
α-helix	278-282	5
β-strand	284-291	8	1
β-strand	297-299	3	4
α-helix	305-307	3
β-strand	312-316	5	1
β-strand	319-322	4	4
α-helix	324-327	4
β-strand	334-338	5	1
β-strand	341-342	2	4
β-strand	349	1	5
β-strand	355-359	5	1
β-strand	366	1	6
β-strand	371	1	5
β-strand	377-379	3	1
β-strand	386	1	6
β-strand	387-390	4	7
α-helix	393-396	4
β-strand	403-405	3	1
β-strand	411-414	4	7
β-strand	426-428	3	1
β-strand	433-435	3	7
β-strand	451-453	3	1
β-strand	460-461	2	8
β-strand	475-477	3	1
β-strand	482-483	2	8
α-helix	484-486	3
β-strand	487-488	2	9
β-strand	500-502	3	1
β-strand	510-511	2	9
β-strand	524-526	3	1
β-strand	534	1	10
α-helix	538-540	3
β-strand	548-550	3	1
β-strand	558	1	10
β-strand	573-575	3	1
β-strand	581	1	11
α-helix	585-587	3
α-helix	588-596	9
β-strand	601	1	1
α-helix	604-606	3
β-strand	608	1	12
β-strand	609	1	11
β-strand	619	1	12
α-helix	620-622	3

Chain B: 15 helices, 51 β-strands

Element	Residues	Length	Sheet
β-strand	30-33	4	13
β-strand	37-39	3	13
β-strand	58-60	3	13
β-strand	68-69	2	14
β-strand	82-84	3	13
β-strand	92-93	2	14
β-strand	106-108	3	13
β-strand	116-117	2	14
β-strand	130-132	3	13
β-strand	154-156	3	13
α-helix	169-172	4
β-strand	179-181	3	13
β-strand	189-190	2	15
α-helix	192-200	9
β-strand	207-209	3	13
β-strand	217-218	2	15
β-strand	227-234	8	13
α-helix	240-248	9
β-strand	254-261	8	13
α-helix	278-282	5
β-strand	284-291	8	13
α-helix	296	1
β-strand	297-299	3	16
α-helix	305-307	3
β-strand	312-316	5	13
β-strand	319-322	4	16
α-helix	324-327	4
β-strand	334-338	5	13
β-strand	341-342	2	16
α-helix	345-347	3
β-strand	349	1	17
β-strand	355-359	5	13
β-strand	362-363	2	16
β-strand	366	1	18
β-strand	371	1	17
β-strand	377-379	3	13
β-strand	386	1	18
β-strand	387-390	4	19
α-helix	393-396	4
β-strand	403-405	3	13
β-strand	411-414	4	19
β-strand	426-428	3	13
β-strand	433-435	3	19
β-strand	451-453	3	13
β-strand	460-461	2	20
β-strand	475-477	3	13
β-strand	482-483	2	20
α-helix	484-486	3
β-strand	487-488	2	21
β-strand	500-502	3	13
β-strand	510-511	2	21
β-strand	524-526	3	13
β-strand	534	1	22
α-helix	538-540	3
β-strand	548-550	3	13
β-strand	558	1	22
α-helix	562-564	3
β-strand	573-575	3	13
β-strand	581-582	2	23
α-helix	585-587	3
α-helix	588-596	9
β-strand	601	1	13
α-helix	604-606	3
β-strand	608	1	24
β-strand	609-611	3	23
β-strand	619	1	24

Chain C: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	22-26	5	25
β-strand	30-36	7	25
β-strand	44-49	6	26
α-helix	51-53	3
β-strand	56-65	10	26
β-strand	75-82	8	25
β-strand	85-86	2	25
α-helix	87-89	3
β-strand	90-93	4	25
α-helix	103-106	4
β-strand	113-122	10	26
β-strand	129-139	11	25
β-strand	144-155	12	25

Chain D: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	22-26	5	27
β-strand	30-36	7	27
β-strand	44-49	6	28
β-strand	56-65	10	28
β-strand	75-82	8	27
β-strand	85-86	2	27
α-helix	87-89	3
β-strand	90-93	4	27
α-helix	103-106	4
β-strand	113-122	10	28
β-strand	129-139	11	27
β-strand	144-155	12	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Toll-like receptor 4	A, B	protein	635	Homo sapiens	O00206 (AlphaFold model)
Lymphocyte antigen 96	C, D	protein	144	Homo sapiens	Q9Y6Y9 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4G8A_1 Toll-like receptor 4 (chains A, B)
RSPWDYKDDDDKLAAANSSIPESWEPCVEVVPNITYQCMELNFYKIPDNLPFSTKNLDLS
FNPLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAF
SGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDL
SSNKIQSIYCTDLRVLHQMPLLNLSLDLSLNPMNFIQPGAFKEIRLHKLTLRNNFDSLNV
MKTCIQGLAGLEVHRLVLGEFRNEGNLEKFDKSALEGLCNLTIEEFRLAYLDYYLDGIID
LFNCLTNVSSFSLVSVTIERVKDFSYNFGWQHLELVNCKFGQFPTLKLKSLKRLTFTSNK
GGNAFSEVDLPSLEFLDLSRNGLSFKGCCSQSDFGTISLKYLDLSFNGVITMSSNFLGLE
QLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNS
FQENFLPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVLNMSHNNFFSLDTFPYKC
LNSLQVLDYSLNHIMTSKKQELQHFPSSLAFLNLTQNDFACTCEHQSFLQWIKDQRQLLV
EVERMECATPSDKQGMPVLSLNITCQMTGHHHHHH

Sequence of entity 2 (C, D), FASTA

>4G8A_2 Lymphocyte antigen 96 (chains C, D)
EAQKQYWVCNSSDASISYTYCDKMQYPISINVNPCIELKGSKGLLHIFYIPRRDLKQLYF
NLYITVNTMNLPKRKEVICRGSDDDYSFCRALKGETVNTTISFSFKGIKFSKGKYKCVVE
AISGSPEEMLFCLEFVILHQPNSN

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4
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
DAO	Lauric acid	C12 H24 O2	2
MYR	Myristic acid	C14 H28 O2	2
KDO	3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid	C8 H14 O8	2

Primary citation

Structural analyses of human Toll-like receptor 4 polymorphisms D299G and T399I. Ohto, U., Yamakawa, N., Akashi-Takamura, S. et al. J Biol Chem (2012) 287:40611-40617. DOI 10.1074/jbc.M112.404608 · 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
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
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

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