6N9O: Human GSDMD

Crystal structure of human GSDMD. Determined by X-ray diffraction at 3.5 Å resolution. Released 5 Jun 2019.

Method: X-ray diffraction
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 11,601
Mol. weight: 211.98 kDa
Released: 5 Jun 2019

Explore 6N9O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6N9O contains 72 α-helices and 64 β-strands across 4 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: 19 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	4-16	13
β-strand	23-24	2	1
α-helix	25	1
β-strand	39-42	4	1
α-helix	43	1
α-helix	45	1
β-strand	55-56	2	1
β-strand	65	1	2
β-strand	88	1	1
β-strand	93	1	3
β-strand	119	1	3
β-strand	121-123	3	1
α-helix	127-136	10
β-strand	139	1	2
α-helix	147-153	7
β-strand	156-165	10	1
β-strand	215-221	7	1
β-strand	229-230	2	1
α-helix	287-299	13
α-helix	306-320	15
α-helix	323-332	10
α-helix	341-344	4
α-helix	347-356	10
β-strand	357	1	4
β-strand	363	1	4
α-helix	365-380	16
α-helix	383-394	12
α-helix	400-411	12
α-helix	413	1
α-helix	425-428	4
α-helix	437-445	9
β-strand	448-449	2	5
β-strand	456-457	2	5
α-helix	460-462	3
α-helix	463-479	17

Chain B: 16 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	4-16	13
β-strand	24	1	6
β-strand	40-42	3	6
α-helix	43-45	3
β-strand	55-56	2	6
α-helix	62-64	3
β-strand	86	1	6
β-strand	121-124	4	6
α-helix	127-136	10
α-helix	147-153	7
β-strand	156-165	10	6
β-strand	170	1	7
β-strand	208	1	7
β-strand	215-223	9	6
β-strand	227-230	4	6
α-helix	287-299	13
α-helix	306-321	16
α-helix	323-332	10
α-helix	341-344	4
α-helix	347-353	7
β-strand	357	1	8
β-strand	363	1	8
α-helix	365-380	16
α-helix	383-395	13
α-helix	400-411	12
α-helix	425-428	4
α-helix	437-445	9
α-helix	463-480	18

Chain C: 19 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	4-15	12
β-strand	23-24	2	9
α-helix	25	1
α-helix	28-31	4
β-strand	38-42	5	9
α-helix	43-45	3
β-strand	47	1	10
β-strand	50	1	10
α-helix	51-53	3
β-strand	55-60	6	9
α-helix	62-64	3
β-strand	65	1	11
β-strand	93	1	12
β-strand	118	1	12
β-strand	121-123	3	9
α-helix	128-136	9
β-strand	139	1	11
α-helix	147-153	7
β-strand	156-166	11	9
β-strand	170	1	13
β-strand	208	1	13
β-strand	212-223	12	9
β-strand	227-230	4	9
α-helix	287-299	13
α-helix	306-320	15
α-helix	323-332	10
α-helix	341-344	4
α-helix	347-356	10
β-strand	357	1	14
β-strand	363	1	14
α-helix	365-380	16
α-helix	383-395	13
α-helix	400-411	12
β-strand	420	1	15
α-helix	437-445	9
β-strand	457	1	15
α-helix	460-462	3
α-helix	463-479	17

Chain D: 18 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	4-14	11
α-helix	23-25	3
α-helix	28-31	4
β-strand	38-42	5	16
α-helix	43-45	3
α-helix	51-53	3
β-strand	55-60	6	16
α-helix	62-64	3
β-strand	65	1	17
β-strand	88	1	16
β-strand	120-123	4	16
α-helix	128-136	9
β-strand	139	1	17
α-helix	147-153	7
β-strand	156-166	11	16
β-strand	170	1	18
β-strand	208	1	18
β-strand	215-223	9	16
β-strand	227-230	4	16
α-helix	287-299	13
α-helix	306-320	15
α-helix	323-332	10
α-helix	341-344	4
α-helix	347-353	7
β-strand	357	1	19
β-strand	363	1	19
α-helix	365-380	16
α-helix	383-395	13
α-helix	400-411	12
β-strand	420-421	2	20
β-strand	434	1	21
β-strand	436	1	21
α-helix	437-445	9
β-strand	456-457	2	20
α-helix	463-479	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gasdermin-D	A, B, C, D	protein	485	Homo sapiens	P57764 (AlphaFold model)

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

>6N9O_1 Gasdermin-D (chains A, B, C, D)
SMGSAFERVVRRVVQELDHGGEFIPVTSLQSSTGFQPYCLVVRKPSSSWFWKPRYKCVNL
SIKDILEPDAAEPDVQRGRSFHFYDAMDGQIQGSVELAAPGQAKIAGGAAVSDSSSTSMN
VYSLSVDPNTWQTLLHERHLRQPEHKVLQQLRSRGDNVYVVTEVLQTQKEVEVTRTHKRE
GSGRFSLPGATCLQGEGQGHLSQKKTVTIPSGSTLAFRVAQLVIDSDLDVLLFPDKKQRT
FQPPATGHKRSTSEGAWPQLPSGLSMMRCLHNFLTDGVPAELAFTEDFQGLRAEVETISK
ELELLDRELCQLLLEGLEGVLRDQLALRALEEALEQGQSLGPVEPLDGPAGAVLECLVLS
SGMLVPELAIPVVYLLGALTMLSETQHKLLAEALESQTLLGPLELVGSLLEQSAPWQERS
TMSLPPGLLGNSWGEGAPAWVLLDECGLELGEDTPHVCWEPQAQGRMCALYASLALLSGL
SQEPH

Primary citation

Crystal Structures of the Full-Length Murine and Human Gasdermin D Reveal Mechanisms of Autoinhibition, Lipid Binding, and Oligomerization. Liu, Z., Wang, C., Yang, J. et al. Immunity (2019) 51:43. DOI 10.1016/j.immuni.2019.04.017 · 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
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
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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