3ULA: TV3 mutant F63W-MD-2-Eritoran complex

Crystal structure of the TV3 mutant F63W-MD-2-Eritoran complex. Determined by X-ray diffraction at 3.6 Å resolution. Released 4 Apr 2012.

Method: X-ray diffraction
Resolution: 3.6 Å
Organisms: Homo sapiens, Eptatretus burgeri
Chains: 4
Atoms: 6,962
Mol. weight: 100.19 kDa
Ligands: E55, NAG
Released: 4 Apr 2012

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

Secondary structure: helices and β-sheets

3ULA contains 13 α-helices and 62 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: 5 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	31-33	3	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	130-132	3	3
α-helix	141-143	3
β-strand	154-156	3	3
α-helix	169-173	5
β-strand	179-181	3	3
β-strand	189-190	2	4
α-helix	193-200	8
β-strand	207-209	3	3
β-strand	217-218	2	4
β-strand	226	1	5
β-strand	230-232	3	3
β-strand	249	1	5
β-strand	254-256	3	3
α-helix	270-278	9
β-strand	283-284	2	3
β-strand	288	1	6
β-strand	295	1	6
α-helix	296-298	3

Chains B and D: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	22-27	6	7
β-strand	30-35	6	7
β-strand	45-49	5	8
β-strand	57-65	9	8
β-strand	75-81	7	7
β-strand	86	1	7
β-strand	90-93	4	7
α-helix	103-106	4
β-strand	113-121	9	8
β-strand	131-139	9	7
β-strand	144-147	4	7
β-strand	150-154	5	7

Chain C: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	31-33	3	9
β-strand	37-39	3	9
β-strand	58-60	3	9
β-strand	68-69	2	10
β-strand	82-84	3	9
β-strand	92-93	2	10
β-strand	106-108	3	9
β-strand	130-132	3	11
α-helix	141-143	3
β-strand	154-156	3	11
α-helix	169-173	5
β-strand	179-181	3	11
β-strand	189-190	2	12
α-helix	193-200	8
β-strand	207-209	3	11
β-strand	217-218	2	12
β-strand	226	1	13
β-strand	230-232	3	11
β-strand	249	1	13
β-strand	254-256	3	11
α-helix	270-278	9
α-helix	280-282	3
β-strand	283-284	2	11
β-strand	288	1	14
β-strand	295	1	14
α-helix	296-298	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Toll-like receptor 4, Variable lymphocyte receptor B	A, C	protein	279	Homo sapiens, Eptatretus burgeri	O00206 (AlphaFold model), Q4G1L2 (AlphaFold model)
Lymphocyte antigen 96	B, D	protein	142	Homo sapiens	Q9Y6Y9 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3ULA_1 Toll-like receptor 4, Variable lymphocyte receptor B (chains A, C)
GSEPCVEVVPNITYQCMELNFYKIPDNLPFSTKNLDLSWNPLRHLGSYSFFSFPELQVLD
LSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQKLVAVETNLASLENF
PIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQMPLL
NLSLDLSLNPMNFIQPGAFKEIRLKELALDTNQLKSVPDGIFDRLTSLQKIWLHTNPWDC
SCPRIDYLSRWLNKNSQKEQGSAKCSGSGKPVRSIICPT

Sequence of entity 2 (B, D), FASTA

>3ULA_2 Lymphocyte antigen 96 (chains B, D)
GSQKQYWVCNSSDASISYTYCDKMQYPISINVNPCIELKGSKGLLHIFYIPRRDLKQLYF
NLYITVNTMNLPKRKEVICRGSDDDYSFCRALKGETVNTTISFSFKGIKFSKGKYKCVVE
AISGSPEEMLFCLEFVILHQPN

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	4

Primary citation

Structure-Based Rational Design of a Toll-like Receptor 4 (TLR4) Decoy Receptor with High Binding Affinity for a Target Protein. Han, J., Kim, H.J., Lee, S.C. et al. PLoS One (2012) 7:e30929-e30929. DOI 10.1371/journal.pone.0030929 · 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
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

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