6KMZ: Caspase-4 P22/P10 C258A

caspase-4 P22/P10 C258A in complex with human GSDMD-C domain. Determined by X-ray diffraction at 3.61 Å resolution. Released 11 Mar 2020.

Method: X-ray diffraction
Resolution: 3.61 Å
Organism: Homo sapiens
Chains: 10
Atoms: 10,693
Mol. weight: 167.28 kDa
Released: 11 Mar 2020

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

Secondary structure: helices and β-sheets

6KMZ contains 47 α-helices and 76 β-strands across 10 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, 8 β-strands

Element	Residues	Length	Sheet
β-strand	291-295	5	10
β-strand	300-304	5	2
β-strand	310	1	4
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	8
β-strand	370	1	1

Chains A and D: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	111-120	10
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	195-199	5
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	231-238	8
β-strand	251-256	6	2
β-strand	262	1	4
β-strand	265-269	5	5
β-strand	282-284	3	6

Chain b: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	291-295	5	5
β-strand	300-304	5	8
β-strand	313-315	3	11
β-strand	319-320	2	11
α-helix	321-333	13
α-helix	339-349	11
β-strand	361-363	3	8
β-strand	365	1	2
β-strand	370	1	7

Chain B: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	111-120	10
β-strand	125	1	7
β-strand	137-142	6	8
α-helix	155-168	14
β-strand	172-177	6	8
α-helix	181-192	12
α-helix	195-199	5
β-strand	203-208	6	8
β-strand	211-212	2	9
β-strand	215-217	3	9
β-strand	228-230	3	9
α-helix	231-238	8
β-strand	251-256	6	8
β-strand	265-269	5	10
β-strand	282-284	3	11

Chain c: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	291-295	5	22
β-strand	300-304	5	14
β-strand	313-315	3	17
β-strand	319-320	2	17
α-helix	321-333	13
α-helix	339-349	11
α-helix	353	1
β-strand	361-363	3	14
β-strand	365	1	19
β-strand	370	1	13

Chain C: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	111-120	10
β-strand	125	1	13
β-strand	137-142	6	14
α-helix	155-168	14
β-strand	172-177	6	14
α-helix	181-192	12
α-helix	195-199	5
β-strand	203-208	6	14
β-strand	211	1	15
β-strand	215-217	3	15
β-strand	228-230	3	15
α-helix	231-238	8
β-strand	251-256	6	14
β-strand	265-268	4	16
β-strand	282-284	3	17

Chain d: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	292-295	4	16
β-strand	300-304	5	19
β-strand	310	1	21
β-strand	313-315	3	23
β-strand	319	1	23
α-helix	321-333	13
α-helix	339-349	11
β-strand	361-363	3	19
β-strand	365	1	14
β-strand	370	1	18

Chain E: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	288-301	14
α-helix	306-321	16
α-helix	348-355	8
β-strand	357	1	12
β-strand	363	1	12
α-helix	365-378	14
α-helix	383-395	13
α-helix	399-411	13
α-helix	437-445	9
α-helix	460-462	3
α-helix	463-479	17

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Caspase-4	A, B, C, D	protein	185	Homo sapiens	P49662 (AlphaFold model)
Gasdermin-D	E	protein	194	Homo sapiens	P57764 (AlphaFold model)
Gasdermin-D	H	protein	195	Homo sapiens	P57764 (AlphaFold model)
Caspase-4	a, b, c, d	protein	88	Homo sapiens	P49662 (AlphaFold model)

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

>6KMZ_1 Caspase-4 (chains A, B, C, D)
ALKLCPHEEFLRLCKERAEEIYPIKERNNRTRLALIICNTEFDHLPPRNGADFDITGMKE
LLEGLDYSVDVEENLTARDMESALRAFATRPEHKSSDSTFLVLMSHGILEGICGTVHDEK
KPDVLLYDTIFQIFNNRNCLSLKDKPKVIIVQAARGANRGELWVRDSPASLEVASSQSSE
NLEED

Sequence of entity 2 (E), FASTA

>6KMZ_2 Gasdermin-D (chains E)
FQGLRAEVETISKELELLDRELCQLLLEGLEGVLRDQLALRALEEALEQGQSLGPVEPLD
GPAGAVLECLVLSSGMLVPELAIPVVYLLGALTMLSETQHKLLAEALESQTLLGPLELVG
SLLEQSAPWQERSTMSLPPGLLGNSWGEGAPAWVLLDECGLELGEDTPHVCWEPQAQGRM
CALYASLALLSGLS

Sequence of entity 3 (H), FASTA

>6KMZ_3 Gasdermin-D (chains H)
DFQGLRAEVETISKELELLDRELCQLLLEGLEGVLRDQLALRALEEALEQGQSLGPVEPL
DGPAGAVLECLVLSSGMLVPELAIPVVYLLGALTMLSETQHKLLAEALESQTLLGPLELV
GSLLEQSAPWQERSTMSLPPGLLGNSWGEGAPAWVLLDECGLELGEDTPHVCWEPQAQGR
MCALYASLALLSGLS

Sequence of entity 4 (a, b, c, d), FASTA

>6KMZ_4 Caspase-4 (chains a, b, c, d)
AVYKTHVEKDFIAFCSSTPHNVSWRDSTMGSIFITQLITCFQKYSWCCHLEEVFRKVQQS
FETPRAKAQMPTIERLSMTRYFYLFPGN

Primary citation

Structural Mechanism for GSDMD Targeting by Autoprocessed Caspases in Pyroptosis. Wang, K., Sun, Q., Zhong, X. et al. Cell (2020) 180:941. DOI 10.1016/j.cell.2020.02.002 · 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
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

Browse structure collections

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