8SPB: Caspase-4/Pro-IL-18 complex

Caspase-4/Pro-IL-18 complex. Determined by electron microscopy at 3.2 Å resolution. Released 22 Nov 2023.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,726
Mol. weight: 111.95 kDa
Released: 22 Nov 2023

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

Secondary structure: helices and β-sheets

8SPB contains 22 α-helices and 63 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: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	111-120	10
β-strand	125	1	12
β-strand	137-142	6	7
α-helix	155-168	14
β-strand	172-176	5	7
α-helix	181-192	12
α-helix	195-199	5
β-strand	203-208	6	7
β-strand	211	1	13
β-strand	215-217	3	13
β-strand	228-230	3	13
α-helix	231-237	7
α-helix	244-246	3
β-strand	251-256	6	7
β-strand	266-269	4	5

Chain A: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	107-110	4
α-helix	111-118	8
β-strand	125	1	1
β-strand	137-142	6	2
α-helix	155-168	14
β-strand	172-177	6	2
α-helix	181-192	12
α-helix	195-197	3
β-strand	203-208	6	2
β-strand	211	1	3
β-strand	215-217	3	3
β-strand	228-230	3	3
α-helix	231-237	7
α-helix	244-246	3
β-strand	251-256	6	2
β-strand	266-269	4	4

Chain b: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	291-294	4	4
β-strand	300-304	5	7
β-strand	313-315	3	14
β-strand	319-320	2	14
α-helix	321-333	13
α-helix	339-349	11
α-helix	353-354	2
β-strand	361-363	3	7
β-strand	365	1	2
β-strand	370	1	12

Chain B: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	291-294	4	5
β-strand	300-304	5	2
β-strand	313-315	3	6
β-strand	319-320	2	6
α-helix	321-333	13
α-helix	339-349	11
β-strand	361-363	3	2
β-strand	365	1	7
β-strand	370	1	1

Chain c: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	18-19	2	15
β-strand	22-23	2	15
β-strand	24-25	2	16
β-strand	33-35	3	14
β-strand	45-46	2	16
β-strand	84-88	5	17
β-strand	97-102	6	17
β-strand	108-111	4	17
α-helix	113-115	3
β-strand	118-120	3	17
β-strand	136-141	6	17
β-strand	148-153	6	17
β-strand	161-165	5	16
β-strand	170-174	5	16
β-strand	186-187	2	16
β-strand	189-190	2	17
α-helix	191-192	2

Chain C: 2 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	8
β-strand	23	1	8
β-strand	24-25	2	9
β-strand	33-35	3	6
β-strand	45-46	2	9
β-strand	85-88	4	10
β-strand	97-100	4	10
β-strand	101-102	2	11
β-strand	108-111	4	11
α-helix	113-115	3
β-strand	118-120	3	11
β-strand	136-141	6	10
β-strand	148-153	6	10
β-strand	161-165	5	9
β-strand	170-174	5	9
β-strand	186-187	2	9
β-strand	189-190	2	10
α-helix	191-192	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Caspase-4 subunit p20	A, a	protein	207	Homo sapiens	P49662 (AlphaFold model)
Caspase-4 subunit p10	B, b	protein	92	Homo sapiens	P49662 (AlphaFold model)
Interleukin-18	C, c	protein	188	Homo sapiens	Q14116 (AlphaFold model)

Sequence of entity 1 (A, a), FASTA

>8SPB_1 Caspase-4 subunit p20 (chains A, a)
MGSSHHHHHHSSGLVPRGSHMENLYFQGGSAGPPESGESTDALKLCPHEEFLRLCKERAE
EIYPIKERNNRTRLALIICNTEFDHLPPRNGADFDITGMKELLEGLDYSVDVEENLTARD
MESALRAFATRPEHKSSDSTFLVLMSHGILEGICGTVHDEKKPDVLLYDTIFQIFNNRNC
LSLKDKPKVIIVQAARGANRGELWVRD

Sequence of entity 2 (B, b), FASTA

>8SPB_2 Caspase-4 subunit p10 (chains B, b)
MGASAVYKTHVEKDFIAFCSSTPHNVSWRDSTMGSIFITQLITCFQKYSWCCHLEEVFRK
VQQSFETPRAKAQMPTIERLSMTRYFYLFPGN

Sequence of entity 3 (C, c), FASTA

>8SPB_3 Interleukin-18 (chains C, c)
VEDNCINFVAMKFIDNTLYFIAEDDENLESDYFGKLESKLSVIRNLNDQVLFIDQGNRPL
FEDMTDSDCRDNAPRTIFIISMYKDSQPRGMAVTISVKCEKISTLSCENKIISFKEMNPP
DNIKDTKSDIIFFQRSVPGHDNKMQFESSSYEGYFLACEKERDLFKLILKKEDELGDRSI
MFTVQNED

Primary citation

Structural insights into cytokine cleavage by inflammatory caspase-4. Devant, P., Dong, Y., Mintseris, J. et al. Nature (2023) 624:451-459. DOI 10.1038/s41586-023-06751-9 · 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+
8J6K 3.12 Å, Crystal structure of pro-interleukin-18 and caspase-4 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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