7WR6: ADP-riboxanated caspase-4

Crystal structure of ADP-riboxanated caspase-4 in complex with Af1521. Determined by X-ray diffraction at 1.96 Å resolution. Released 25 Jan 2023.

Method: X-ray diffraction
Resolution: 1.96 Å
Organisms: Homo sapiens, Archaeoglobus fulgidus
Chains: 2
Atoms: 3,726
Mol. weight: 54.48 kDa
Ligands: 5ZY
Released: 25 Jan 2023

Explore 7WR6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7WR6 contains 21 α-helices and 18 β-strands across 2 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: 14 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	106-110	5
α-helix	111-120	10
α-helix	122-124	3
β-strand	125	1	1
α-helix	126-130	5
α-helix	131-133	3
β-strand	136-142	7	2
α-helix	155-168	14
β-strand	171-177	7	2
α-helix	181-192	12
α-helix	195-197	3
β-strand	203-210	8	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	251-258	8	2
α-helix	293-296	4
β-strand	300-305	6	2
α-helix	321-333	13
α-helix	339-349	11
α-helix	356-358	3
β-strand	361-363	3	2
β-strand	370	1	1

Chain B: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	4
β-strand	12-18	7	4
α-helix	21-23	3
β-strand	28-33	6	4
α-helix	42-52	11
α-helix	55-70	16
β-strand	81-84	4	4
α-helix	86-91	6
β-strand	95-100	6	4
α-helix	110-130	21
β-strand	134-137	4	4
α-helix	149-162	14
β-strand	170-175	6	4
α-helix	178-190	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Caspase-4	A	protein	280	Homo sapiens	P49662 (AlphaFold model)
ADP-ribose glycohydrolase AF_1521	B	protein	200	Archaeoglobus fulgidus	O28751 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7WR6_1 Caspase-4 (chains A)
SGRPSTDALKLCPHEEFLRLCKERAEEIYPIKERNNRTRLALIICNTEFDHLPPRNGADF
DITGMKELLEGLDYSVDVEENLTARDMESALRAFATRPEHKSSDSTFLVLMSHGILEGIC
GTVHDEKKPDVLLYDTIFQIFNNRNCLSLKDKPKVIIVQAARGANRGELWVRDSPASLEV
ASSQSSENLEEDAVYKTHVEKDFIAFCSSTPHNVSWRDSTMGSIFITQLITCFQKYSWCC
HLEEVFRKVQQSFETPRAKAQMPTIERLSMTRYFYLFPGN

Sequence of entity 2 (B), FASTA

>7WR6_2 ADP-ribose glycohydrolase AF_1521 (chains B)
GPLGSGRPMEVLFEAKVGDITLKLAQGDITQYPAKAIVNAANKRLEHGGGVAYAIAKACA
GDAGLYTEISKKAMREQFGRDYIDHGEVVVTPAMNLEERGIKYVFHTVGPICSGMWSEEL
KEKLYKAFLGPLEKAEEMGVESIAFPAVSAGIYGCDLEKVVETFLEAVKNFKGSAVKEVA
LVIYDRKSAEVALKVFERSL

Ligands and cofactors

ID	Name	Formula	Copies
5ZY	[[(3~{a}~{S},5~{R},6~{R},6~{a}~{R})-2-azanylidene-3-[(4~{R})-4-azanyl-5-oxidany…	C21 H32 N8 O14 P2	1

Primary citation

Structural mechanisms of calmodulin activation of Shigella effector OspC3 to ADP-riboxanate caspase-4/11 and block pyroptosis. Hou, Y., Zeng, H., Li, Z. et al. Nat Struct Mol Biol (2023) 30:261-272. DOI 10.1038/s41594-022-00888-3 · PubMed

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

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
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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