5WQT: Protein involved in pyroptosis

Structure of a protein involved in pyroptosis. Determined by X-ray diffraction at 2.64 Å resolution. Released 4 Oct 2017.

Method: X-ray diffraction
Resolution: 2.64 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,959
Mol. weight: 45.68 kDa
Ligands: CIT
Released: 4 Oct 2017

Explore 5WQT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5WQT contains 25 α-helices and 8 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: 13 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	12-27	16
α-helix	31-44	14
α-helix	48-57	10
α-helix	72-79	8
β-strand	82	1	1
α-helix	83	1
α-helix	86	1
β-strand	88	1	1
α-helix	90-103	14
α-helix	108-119	12
α-helix	124-136	13
β-strand	144-146	3	2
α-helix	150-153	4
α-helix	162-170	9
β-strand	173-174	2	2
β-strand	181-183	3	2
α-helix	185-187	3
α-helix	188-204	17

Chain B: 12 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
α-helix	12-27	16
α-helix	31-45	15
α-helix	48-58	11
α-helix	72-78	7
α-helix	90-103	14
α-helix	108-120	13
α-helix	124-137	14
β-strand	144-146	3	3
α-helix	150-153	4
α-helix	162-170	9
β-strand	173-174	2	3
β-strand	181-183	3	3
α-helix	185-187	3
α-helix	188-205	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gasdermin-D	A, B	protein	209	Homo sapiens	P57764 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5WQT_1 Gasdermin-D (chains A, B)
GVPAEGAFTEDFQGLRAEVETISKELELLDRELCQLLLEGLEGVLRDQLALRALEEALEQ
GQSLGPVEPLDGPAGAVLECLVLSSGMLVPELAIPVVYLLGALTMLSETQHKLLAEALES
QTLLGPLELVGSLLEQSAPWQERSTMSLPPGLLGNSWGEGAPAWVLLDECGLELGEDTPH
VCWEPQAQGRMCALYASLALLSGLSQEPH

Ligands and cofactors

ID	Name	Formula	Copies
CIT	Citric acid	C6 H8 O7	2

Water and common crystallization additives (GOL) are not listed.

Primary citation

Structure insight of GSDMD reveals the basis of GSDMD autoinhibition in cell pyroptosis. Kuang, S., Zheng, J., Yang, H. et al. Proc Natl Acad Sci U S A (2017) 114:10642-10647. DOI 10.1073/pnas.1708194114 · PubMed

Other PDB entries of the same protein (UniProt P57764 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9E0V 1.64 Å, GSDMD bound to a peptide
7Z1X 1.86 Å, Crystal structure of human Gasdermin D complexed with nanobodies VHH-2 and VHH-6
5NH1 2.04 Å, Structure of the C-terminal domain of human Gasdermin D
6KN0 2.79 Å, caspase-1 P20/P10 C285A in complex with human GSDMD-C domain
6AO4 2.9 Å, Crystal structure of the human gasdermin D C-terminal domain
23BD 3.4 Å, Caspase-4 p22/p10 and human GSDMD complex
6N9O 3.5 Å, Crystal structure of human GSDMD
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
6VFE 3.9 Å, Gasdermin D pore

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