8J6K: Pro-interleukin-18 and caspase-4 complex

Crystal structure of pro-interleukin-18 and caspase-4 complex. Determined by X-ray diffraction at 3.12 Å resolution. Released 29 Nov 2023.

Method: X-ray diffraction
Resolution: 3.12 Å
Organisms: Homo sapiens, Shigella flexneri
Chains: 4
Atoms: 4,269
Mol. weight: 70.56 kDa
Released: 29 Nov 2023

Explore 8J6K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8J6K contains 25 α-helices and 31 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: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	300-304	5	2
β-strand	310	1	4
β-strand	313-315	3	5
β-strand	319-320	2	5
α-helix	321-333	13
α-helix	339-349	11
β-strand	361-363	3	2
β-strand	370	1	1

Chain A: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	111-120	10
β-strand	125	1	1
α-helix	131-133	3
β-strand	137-142	6	2
α-helix	155-167	13
β-strand	172-177	6	2
α-helix	181-192	12
α-helix	195-199	5
β-strand	203-208	6	2
β-strand	211	1	3
β-strand	215-217	3	3
α-helix	218	1
β-strand	228-230	3	3
α-helix	231-237	7
α-helix	244-246	3
β-strand	251-256	6	2
β-strand	262	1	4

Chain B: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	10-19	10	6
β-strand	22-27	6	6
β-strand	33-35	3	5
β-strand	44-47	4	6
α-helix	50-52	3
β-strand	54	1	7
β-strand	82-86	5	7
β-strand	97-98	2	6
β-strand	99-103	5	7
β-strand	107-111	5	7
α-helix	113-115	3
β-strand	118-121	4	7
β-strand	137-141	5	6
α-helix	142	1
β-strand	148-153	6	6
β-strand	159-165	7	6
β-strand	170-176	7	6
β-strand	185-190	6	6

Chain C: 12 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	348-353	6
α-helix	357-363	7
α-helix	367-379	13
α-helix	383-392	10
α-helix	397-404	8
α-helix	410-414	5
α-helix	417-422	6
α-helix	425-427	3
α-helix	428-436	9
α-helix	444-446	3
β-strand	449	1	2
α-helix	455-462	8
α-helix	465-473	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Caspase-4 subunit p20	A	protein	169	Homo sapiens	P49662 (AlphaFold model)
Caspase-4 subunit p10	a	protein	88	Homo sapiens	P49662 (AlphaFold model)
Interleukin-18	B	protein	194	Homo sapiens	Q14116 (AlphaFold model)
Arginine ADP-riboxanase OspC3	C	protein	161	Shigella flexneri	A0A0H2US87 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8J6K_1 Caspase-4 subunit p20 (chains A)
STDALKLCPHEEFLRLCKERAEEIYPIKERNNRTRLALIICNTEFDHLPPRNGADFDITG
MKELLEGLDYSVDVEENLTARDMESALRAFATRPEHKSSDSTFLVLMSHGILEGICGTVH
DEKKPDVLLYDTIFQIFNNRNCLSLKDKPKVIIVQAARGANRGELWVRD

Sequence of entity 2 (a), FASTA

>8J6K_2 Caspase-4 subunit p10 (chains a)
AVYKTHVEKDFIAFCSSTPHNVSWRDSTMGSIFITQLITCFQKYSWCCHLEEVFRKVQQS
FETPRAKAQMPTIERLSMTRYFYLFPGN

Sequence of entity 3 (B), FASTA

>8J6K_3 Interleukin-18 (chains B)
SMAAEPVEDNCINFVAMKFIDNTLYFIAEDDENLESDYFGKLESKLSVIRNLNDQVLFID
QGNRPLFEDMTDSDCRDNAPRTIFIISMYKDSQPRGMAVTISVKCEKISTLSCENKIISF
KEMNPPDNIKDTKSDIIFFQRSVPGHDNKMQFESSSYEGYFLACEKERDLFKLILKKEDE
LGDRSIMFTVQNED

Sequence of entity 4 (C), FASTA

>8J6K_4 Arginine ADP-riboxanase OspC3 (chains C)
GPLGSGRPMLSTDNFKKIKLRDISLEDAIKASNYEEINNKVTDKKMAHQALAYSLGNKKA
DIALYLLSKFNFTKQDVAEMEKMKNNRYCNLYDVEYLLSKDGANYKVLEYFINNGLVDVN
KKFQKVNSGDTMLDNAMKSKDSKMIDFLLKNGAILGKRFEI

Primary citation

Recognition and maturation of IL-18 by caspase-4 noncanonical inflammasome. Shi, X., Sun, Q., Hou, Y. et al. Nature (2023) 624:442-450. DOI 10.1038/s41586-023-06742-w · PubMed

Other PDB entries of the same protein (UniProt P49662 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7WR6 1.96 Å, Crystal structure of ADP-riboxanated caspase-4 in complex with Af1521
7WR1 2.13 Å, P32 of caspase-4 C258A mutant in complex with OspC3 C-terminal ankyrin-repeat domain
6NRY 2.18 Å, Crystal structure of human caspase-4
7WR4 2.75 Å, Crystal structure of OspC3-calmodulin-caspase-4 complex
7WR0 2.8 Å, P32 of caspase-4 C258A mutant
7WR5 3.1 Å, Crystal structure of OspC3-calmodulin-caspase-4 complex binding with 2'-aF-NAD+
8SPB 3.2 Å, Caspase-4/Pro-IL-18 complex
23BD 3.4 Å, Caspase-4 p22/p10 and human GSDMD complex
23BB 3.6 Å, Caspase-4 p20/p10 and human GSDMD
6KMZ 3.61 Å, caspase-4 P22/P10 C258A in complex with human GSDMD-C domain

Browse structure collections

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