6KN9: Interleukin-18 receptor accessory protein

Crystal structure of human interleukin 18 receptor beta extracellular domain in complex with an antagonistic scFv. Determined by X-ray diffraction at 3.3 Å resolution. Released 12 Feb 2020.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 6
Atoms: 9,768
Mol. weight: 198.1 kDa
Ligands: NAG
Released: 12 Feb 2020

Explore 6KN9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6KN9 contains 16 α-helices and 127 β-strands across 6 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: 3 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	30-34	5	1
β-strand	42-45	4	2
β-strand	105-106	2	2
β-strand	110-113	4	2
β-strand	125-126	2	3
β-strand	141-142	2	3
β-strand	143-147	5	1
β-strand	162-166	5	1
β-strand	171-174	4	4
β-strand	190-193	4	1
β-strand	196-199	4	1
β-strand	205-208	4	4
α-helix	213-215	3
β-strand	217-227	11	1
β-strand	230-243	14	1
β-strand	252-255	4	5
β-strand	260-263	4	6
β-strand	269-277	9	5
β-strand	286-293	8	6
β-strand	296-299	4	6
α-helix	303-305	3
β-strand	306-310	5	5
β-strand	315-323	9	5
α-helix	329-331	3
β-strand	334-341	8	6
β-strand	344-354	11	6

Chain B: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	30-35	6	7
β-strand	42-44	3	8
β-strand	106	1	8
β-strand	111-113	3	8
β-strand	124-126	3	7
β-strand	141-148	8	7
β-strand	164-166	3	9
β-strand	171-174	4	10
α-helix	176-178	3
β-strand	192-193	2	11
β-strand	196	1	11
β-strand	205-208	4	10
α-helix	213-215	3
β-strand	217-220	4	11
β-strand	238-240	3	11
β-strand	241-243	3	9
β-strand	252-255	4	12
β-strand	260-263	4	13
β-strand	269-277	9	12
β-strand	286-292	7	13
β-strand	298-299	2	13
α-helix	302-305	4
β-strand	306-310	5	12
β-strand	315-323	9	12
α-helix	329-332	4
β-strand	334-340	7	13
β-strand	345-354	10	13

Chain C: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	30-34	5	14
β-strand	42-45	4	15
β-strand	105-106	2	15
β-strand	110-113	4	15
β-strand	122	1	14
β-strand	126	1	16
β-strand	142	1	16
β-strand	143-147	5	14
β-strand	162-166	5	14
β-strand	171-174	4	17
β-strand	190-193	4	14
β-strand	196-199	4	14
β-strand	205-208	4	17
α-helix	213-215	3
β-strand	217-226	10	14
β-strand	231-243	13	14
α-helix	250-251	2
β-strand	252-255	4	18
β-strand	260-263	4	19
β-strand	269-277	9	18
β-strand	286-293	8	19
β-strand	296-299	4	19
α-helix	302-305	4
β-strand	306-310	5	18
β-strand	315-323	9	18
α-helix	329-331	3
β-strand	334-340	7	19
β-strand	345-354	10	19

Chain D: 2 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	20
β-strand	11	1	21
β-strand	17-25	9	20
α-helix	29-31	3
β-strand	32-39	8	22
β-strand	45-52	8	22
β-strand	57-60	4	22
β-strand	69-73	5	20
β-strand	78-84	7	20
β-strand	92-100	9	22
β-strand	110-113	4	22
β-strand	117-119	3	22
β-strand	120	1	21
β-strand	149-150	2	23
β-strand	159-164	6	24
β-strand	174-178	5	23
β-strand	185-189	5	23
β-strand	193-194	2	23
β-strand	202-205	4	24
β-strand	210-215	6	24
α-helix	220-222	3
β-strand	225-231	7	23
β-strand	239-241	3	23
β-strand	245-246	2	23

Chain E: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	25
β-strand	22-24	3	25
β-strand	32-38	7	26
β-strand	51	1	26
β-strand	52	1	27
β-strand	57	1	27
β-strand	70-73	4	25
β-strand	78-81	4	25
β-strand	94-100	7	26
β-strand	110-113	4	26
β-strand	175-178	4	28
β-strand	185-189	5	28
β-strand	193-194	2	28
α-helix	195	1
β-strand	225-228	4	28

Chain F: 2 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	29
β-strand	10-11	2	30
β-strand	18-25	8	29
α-helix	29-31	3
β-strand	32-39	8	30
β-strand	45-52	8	30
β-strand	57-60	4	30
β-strand	69-73	5	29
β-strand	78-83	6	29
β-strand	92-100	9	30
β-strand	113	1	30
β-strand	117-120	4	30
β-strand	149-150	2	31
β-strand	159-162	4	32
β-strand	174-178	5	31
β-strand	185-189	5	31
β-strand	193-194	2	31
β-strand	202-205	4	32
β-strand	212-215	4	32
α-helix	220-222	3
β-strand	225-231	7	31
β-strand	239-241	3	31
β-strand	245-246	2	31

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interleukin-18 receptor accessory protein	A, B, C	protein	337	Homo sapiens	O95256 (AlphaFold model)
scFv	D, E, F	protein	257	Homo sapiens

Sequence of entity 1 (A, B, C), FASTA

>6KN9_1 Interleukin-18 receptor accessory protein (chains A, B, C)
FNISGCSTKKLLWTYSTRSEEEFVLFCDLPEPQKSHFCHRNRLSPKQVPEHLPFMGSNDL
SDVQWYQQPSNGDPLEDIRKSYPHIIQDKCTLHFLTPGVNNSGSYICRPKMIKSPYDVAC
CVKMILEVKPQTNASCEYSASHKQDLLLGSTGSISCPSLSCQSDAQSPAVTWYKNGKLLS
VERSNRIVVDEVYDYHQGTYVCDYTQSDTVSSWTVRAVVQVRTIVGDTKLKPDILDPVED
TLEVELGKPLTISCKARFGFERVFNPVIKWYIKDSDLEWEVSVPEAKSIKSTLKDEIIER
NIILEKVTQRDLRRKFVCFVQNSIGNTTQSVQLKEKR

Sequence of entity 2 (D, E, F), FASTA

>6KN9_2 scFv (chains D, E, F)
GPLDPEVQLVESGGGLVQPGGSLRLSCAASGFNLYYSSMHWVRQAPGKGLEWVASIYSSY
GYTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARSSFSHGYGWYGLDYWGQ
GTLVTVSSSSGGGGSGGGGSGGGGSDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAW
YQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQYGYHY
AGLITFGQGTKVEIKRT

Ligands and cofactors

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

Primary citation

A Synthetic Human Antibody Antagonizes IL-18R beta Signaling Through an Allosteric Mechanism. Liu, S., Miersch, S., Li, P. et al. J Mol Biol (2020) 432:1169-1182. DOI 10.1016/j.jmb.2020.01.012 · PubMed

Other PDB entries of the same protein (UniProt O95256 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7FCH 1.88 Å, IL-18Rbeta TIR domain
3WO4 3.1 Å, Crystal structure of the IL-18 signaling ternary complex

Browse structure collections

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