2Z65: Human TLR4 TV3 hybrid-MD-2-Eritoran complex

Crystal structure of the human TLR4 TV3 hybrid-MD-2-Eritoran complex. Determined by X-ray diffraction at 2.7 Å resolution. Released 18 Sept 2007.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Homo sapiens, Eptatretus burgeri
Chains: 4
Atoms: 7,096
Mol. weight: 98.97 kDa
Ligands: E55, NAG
Released: 18 Sept 2007

Explore 2Z65 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2Z65 contains 15 α-helices and 66 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: 4 helices, 23 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	117	1	2
β-strand	130-132	3	1
β-strand	154-156	3	1
α-helix	169-172	4
β-strand	179-181	3	1
β-strand	189-190	2	3
α-helix	193-200	8
β-strand	206-209	4	1
β-strand	217-218	2	3
β-strand	226-227	2	4
β-strand	228-232	5	1
β-strand	249-250	2	4
β-strand	254-256	3	1
β-strand	262	1	5
α-helix	270-278	9
β-strand	283-284	2	1
β-strand	288	1	6
β-strand	289	1	5
β-strand	295	1	6
α-helix	296-298	3

Chain B: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	30-33	4	7
β-strand	37-39	3	7
β-strand	58-60	3	7
β-strand	68-69	2	8
β-strand	82-84	3	7
β-strand	92-93	2	8
β-strand	106-108	3	7
β-strand	117	1	8
β-strand	130-132	3	7
α-helix	141-143	3
β-strand	154-156	3	7
α-helix	169-172	4
β-strand	179-181	3	7
β-strand	189-190	2	9
α-helix	193-200	8
β-strand	206-209	4	7
β-strand	217-218	2	9
β-strand	226-227	2	10
β-strand	228-232	5	7
β-strand	249-250	2	10
β-strand	254-256	3	7
β-strand	262	1	11
α-helix	270-278	9
β-strand	283-284	2	7
β-strand	288	1	12
β-strand	289	1	11
β-strand	295	1	12
α-helix	296-298	3

Chain C: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	22-26	5	13
β-strand	31-36	6	13
β-strand	45-49	5	14
α-helix	51-53	3
β-strand	56-65	10	14
β-strand	75-82	8	13
β-strand	85-86	2	13
β-strand	90-93	4	13
α-helix	103-106	4
β-strand	113-122	10	14
α-helix	123-124	2
α-helix	130	1
β-strand	131-139	9	13
β-strand	144-154	11	13

Chain D: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	22-26	5	15
β-strand	31-36	6	15
β-strand	45-49	5	16
α-helix	51-53	3
β-strand	56-65	10	16
β-strand	75-82	8	15
β-strand	85-86	2	15
β-strand	90-93	4	15
α-helix	103-106	4
β-strand	113-122	10	16
β-strand	131-139	9	15
β-strand	144-154	11	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Toll-like receptor 4, Variable lymphocyte receptor B	A, B	protein	276	Homo sapiens, Eptatretus burgeri	O00206 (AlphaFold model), Q4G1L2 (AlphaFold model)
Lymphocyte antigen 96	C, D	protein	140	Homo sapiens	Q9Y6Y9 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2Z65_1 Toll-like receptor 4, Variable lymphocyte receptor B (chains A, B)
EPCVEVVPNITYQCMELNFYKIPDNLPFSTKNLDLSFNPLRHLGSYSFFSFPELQVLDLS
RCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQKLVAVETNLASLENFPI
GHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQMPLLNL
SLDLSLNPMNFIQPGAFKEIRLKELALDTNQLKSVPDGIFDRLTSLQKIWLHTNPWDCSC
PRIDYLSRWLNKNSQKEQGSAKCSGSGKPVRSIICP

Sequence of entity 2 (C, D), FASTA

>2Z65_2 Lymphocyte antigen 96 (chains C, D)
QKQYWVCNSSDASISYTYCDKMQYPISINVNPCIELKGSKGLLHIFYIPRRDLKQLYFNL
YITVNTMNLPKRKEVICRGSDDDYSFCRALKGETVNTTISFSFKGIKFSKGKYKCVVEAI
SGSPEEMLFCLEFVILHQPN

Ligands and cofactors

ID	Name	Formula	Copies
E55	3-O-decyl-2-deoxy-6-O-{2-deoxy-3-O-[(3R)-3-methoxydecyl]-6-O-methyl-2-[(11Z)-oc…	C66 H126 N2 O19 P2	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

Primary citation

Crystal Structure of the TLR4-MD-2 Complex with Bound Endotoxin Antagonist Eritoran. Kim, H.M., Park, B.S., Kim, J.-I. et al. Cell (2007) 130:906-917. DOI 10.1016/j.cell.2007.08.002 · 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
4G8A 2.4 Å, Crystal structure of human TLR4 polymorphic variant D299G and T399I in complex with MD-2…
3UL9 2.45 Å, structure of the TV3 mutant M41E
3UL8 2.5 Å, Crystal structure of the TV3 mutant V134L
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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