5NH1: C-terminal domain of human Gasdermin D

Structure of the C-terminal domain of human Gasdermin D. Determined by X-ray diffraction at 2.04 Å resolution. Released 20 Sept 2017.

Method: X-ray diffraction
Resolution: 2.04 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,656
Mol. weight: 22.17 kDa
Released: 20 Sept 2017

Explore 5NH1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5NH1 contains 13 α-helices and 5 β-strands across 1 chain. 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	287-298	12
α-helix	299-301	3
α-helix	306-320	15
α-helix	323-333	11
α-helix	341-344	4
α-helix	347-355	9
β-strand	357	1	1
β-strand	363	1	1
α-helix	365-378	14
α-helix	383-394	12
α-helix	399-411	13
β-strand	419-421	3	2
α-helix	425-428	4
α-helix	437-443	7
β-strand	448-449	2	2
β-strand	456-458	3	2
α-helix	460-462	3
α-helix	463-479	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gasdermin-D	A	protein	207	Homo sapiens	P57764 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5NH1_1 Gasdermin-D (chains A)
PAEGAFTEDFQGLRAEVETISKELELLDRELCQLLLEGLEGVLRDQLALRALEEALEQGQ
SLGPVEPLDGPAGAVLECLVLSSGMLVPELAIPVVYLLGALTMLSETQHKLLAEALESQT
LLGPLELVGSLLEQSAPWQERSTMSLPPGLLGNSWGEGAPAWVLLDECGLELGEDTPHVC
WEPQAQGRMCALYASLALLSGLSQEPH

Primary citation

Insights into Gasdermin D activation from the crystal structure of its C-terminal domain. Anton, L., Sborgi, L., Hiller, S. et al. bioRxiv (2017). DOI 10.1101/187211

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
5WQT 2.64 Å, Structure of a protein involved in pyroptosis
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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