3UL9: TV3 mutant M41E

structure of the TV3 mutant M41E. Determined by X-ray diffraction at 2.45 Å resolution. Released 23 May 2012.

Method: X-ray diffraction
Resolution: 2.45 Å
Organisms: Homo sapiens, Eptatretus burgeri
Chains: 1
Atoms: 2,303
Mol. weight: 32.52 kDa
Ligands: FUL, NAG
Released: 23 May 2012

Explore 3UL9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3UL9 contains 3 α-helices and 21 β-strands across 1 chain. 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: 3 helices, 21 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
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	192-195	4
β-strand	207-209	3	1
β-strand	217-218	2	3
β-strand	230-232	3	1
β-strand	254-256	3	1
β-strand	262	1	4
α-helix	270-277	8
β-strand	283-284	2	1
β-strand	288	1	5
β-strand	289	1	4
β-strand	295	1	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Toll-like receptor 4, Variable lymphocyte receptor B	A	protein	278	Homo sapiens, Eptatretus burgeri	O00206 (AlphaFold model), Q4G1L2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3UL9_1 Toll-like receptor 4, Variable lymphocyte receptor B (chains A)
GSPCVEVVPNITYQCEELNFYKIPDNLPFSTKNLDLSFNPLRHLGSYSFFSFPELQVLDL
SRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQKLVAVETNLASLENFP
IGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQMPLLN
LSLDLSLNPMNFIQPGAFKEIRLKELALDTNQLKSVPDGIFDRLTSLQKIWLHTNPWDCS
CPRIDYLSRWLNKNSQKEQGSAKCSGSGKPVRSIICPT

Ligands and cofactors

ID	Name	Formula	Copies
FUL	beta-L-fucopyranose	C6 H12 O5	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Water and common crystallization additives (SO4) are not listed.

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…
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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