3WO4: IL-18 signaling ternary complex

Crystal structure of the IL-18 signaling ternary complex. Determined by X-ray diffraction at 3.1 Å resolution. Released 17 Dec 2014.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 3
Atoms: 6,030
Mol. weight: 98.47 kDa
Ligands: NAG
Released: 17 Dec 2014

Explore 3WO4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3WO4 contains 17 α-helices and 61 β-strands across 3 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, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-13	12	1
α-helix	18	1
β-strand	19-22	4	1
β-strand	28-31	4	1
α-helix	35-40	6
β-strand	47-54	8	1
β-strand	60-67	8	1
β-strand	71-75	5	1
α-helix	77-79	3
β-strand	82-84	3	1
α-helix	87-89	3
β-strand	91-92	2	1
β-strand	101-106	6	1
β-strand	109-117	9	1
β-strand	123-130	8	1
β-strand	133-140	8	1
α-helix	147-149	3
β-strand	151-155	5	1

Chain B: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	27-31	5	2
β-strand	36-39	4	3
α-helix	49-51	3
β-strand	55-59	5	2
β-strand	66-67	2	2
α-helix	68-69	2
β-strand	76-79	4	3
β-strand	82-85	4	3
α-helix	90-92	3
β-strand	94-100	7	2
β-strand	103-112	10	2
α-helix	113-114	2
β-strand	125	1	4
β-strand	128-131	4	4
β-strand	135-139	5	5
β-strand	149-156	8	4
β-strand	159-160	2	4
β-strand	170-174	5	5
α-helix	177-179	3
β-strand	181-191	11	4
β-strand	194-207	14	4
α-helix	211-215	5
β-strand	216-217	2	6
β-strand	222-226	5	7
β-strand	233-241	9	6
β-strand	246-250	5	7
β-strand	261-263	3	6
α-helix	264-266	3
β-strand	267-271	5	6
β-strand	275-284	10	6
α-helix	289-291	3
β-strand	295-302	8	7
β-strand	305-314	10	7

Chain C: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	32-36	5	8
β-strand	41-44	4	9
β-strand	106-107	2	9
β-strand	110-114	5	9
β-strand	122-126	5	10
β-strand	141-145	5	10
β-strand	146-149	4	8
β-strand	162-166	5	8
β-strand	171-174	4	11
α-helix	176-178	3
β-strand	189-193	5	8
β-strand	196-197	2	8
β-strand	205-208	4	11
α-helix	213-215	3
β-strand	217-224	8	8
β-strand	233-243	11	8
α-helix	244-247	4
β-strand	252-255	4	12
β-strand	260-263	4	13
β-strand	269-278	10	12
β-strand	286-293	8	13
β-strand	296-299	4	13
β-strand	306-310	5	12
β-strand	314-323	10	12
α-helix	328-331	4
β-strand	334-341	8	13
β-strand	344-354	11	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interleukin-18	A	protein	157	Homo sapiens	Q14116 (AlphaFold model)
Interleukin-18 receptor 1	B	protein	312	Homo sapiens	Q13478 (AlphaFold model)
Interleukin-18 receptor accessory protein	C	protein	344	Homo sapiens	O95256 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3WO4_1 Interleukin-18 (chains A)
YFGKLESKLSVIRNLNDQVLFIDQGNRPLFEDMTDSDCRDNAPRTIFIISMYKDSQPRGM
AVTISVKCEKISTLSCENKIISFKEMNPPDNIKDTKSDIIFFQRSVPGHDNKMQFESSSY
EGYFLACEKERDLFKLILKKEDELGDRSIMFTVQNED

Sequence of entity 2 (B), FASTA

>3WO4_2 Interleukin-18 receptor 1 (chains B)
GPESCTSRPHITVVEGEPFYLKHCSCSLAHEIETTTKSWYKSSGSQEHVELNPRSSSRIA
LHDCVLEFWPVELNDTGSYFFQMKNYTQKWKLNVIRRNKHSCFTERQVTSKIVEVKKFFQ
ITCENSYYQTLVNSTSLYKNCKKLLLENNKNPTIKKNAEFEDQGYYSCVHFLHHNGKLFN
ITKTFNITIVEDRSNIVPVLLGPKLNHVAVELGKNVRLNCSALLNEEDVIYWMFGEENGS
DPNIHEEKEMRIMTPEGKWHASKVLRIENIGESNLNVLYNCTVASTGGTDTKSFILVRKA
DMADIPGHVFTR

Sequence of entity 3 (C), FASTA

>3WO4_3 Interleukin-18 receptor accessory protein (chains C)
GPERIKGFNISGCSTKKLLWTYSTRSEEEFVLFCDLPEPQKSHFCHRNRLSPKQVPEHLP
FMGSNDLSDVQWYQQPSNGDPLEDIRKSYPHIIQDKCTLHFLTPGVNNSGSYICRPKMIK
SPYDVACCVKMILEVKPQTNASCEYSASHKQDLLLGSTGSISCPSLSCQSDAQSPAVTWY
KNGKLLSVERSNRIVVDEVYDYHQGTYVCDYTQSDTVSSWTVRAVVQVRTIVGDTKLKPD
ILDPVEDTLEVELGKPLTISCKARFGFERVFNPVIKWYIKDSDLEWEVSVPEAKSIKSTL
KDEIIERNIILEKVTQRDLRRKFVCFVQNSIGNTTQSVQLKEKR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

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

Primary citation

The structural basis for receptor recognition of human interleukin-18. Tsutsumi, N., Kimura, T., Arita, K. et al. Nat Commun (2014) 5:5340-5340. DOI 10.1038/ncomms6340 · PubMed

Other PDB entries of the same protein (UniProt Q14116 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2VXT 1.49 Å, Crystal structure of human IL-18 complexed to murine reference antibody 125-2H Fab
9OD9 1.6 Å, Structure of disulfide-stabilized IL-18 variant
4EKX 1.75 Å, Crystal Structure of YLDV 14L IL-18 Binding Protein in Complex with Human IL-18
7AL7 1.8 Å, The Crystal Structure of Human IL-18 in Complex With Human IL-18 Binding Protein
9OD7 1.9 Å, Structure of disulfide-stabilized IL-18 variant
4XFS 1.91 Å, Structure of IL-18 SER Mutant I
3F62 2.0 Å, Crystal Structure of Human IL-18 in complex with Ectromelia virus IL-18 Binding Protein
4XFT 2.0 Å, Structure of IL-18 SER Mutant III
4HJJ 2.1 Å, Structure Reveals Function of the Dual Variable Domain Immunoglobulin (DVD-Ig) Molecule
3WO2 2.33 Å, Crystal structure of human interleukin-18
4EEE 2.71 Å, Crystal Structure of YLDV 14L IL-18 Binding Protein in Complex with Human IL-18
4R6U 2.8 Å, IL-18 receptor complex

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