7Z1X: Human Gasdermin D

Crystal structure of human Gasdermin D complexed with nanobodies VHH-2 and VHH-6. Determined by X-ray diffraction at 1.86 Å resolution. Released 6 Sept 2023.

Method: X-ray diffraction
Resolution: 1.86 Å
Organisms: Homo sapiens, Lama glama
Chains: 6
Atoms: 10,263
Mol. weight: 157.39 kDa
Released: 6 Sept 2023

Explore 7Z1X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Z1X contains 52 α-helices and 82 β-strands across 6 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: 23 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	4-16	13
α-helix	22	1
β-strand	23-24	2	1
α-helix	25	1
β-strand	38-42	5	1
α-helix	43-45	3
α-helix	52-54	3
β-strand	55-60	6	1
α-helix	61-64	4
β-strand	65	1	2
α-helix	70-74	5
β-strand	75-81	7	1
β-strand	119-124	6	1
α-helix	127-136	10
β-strand	139	1	2
α-helix	143-144	2
α-helix	145-152	8
β-strand	156-166	11	1
β-strand	169-171	3	3
β-strand	206-208	3	3
α-helix	209	1
β-strand	213-223	11	1
β-strand	227-230	4	1
β-strand	240	1	1
α-helix	286-298	13
α-helix	299-301	3
α-helix	306-320	15
α-helix	323-332	10
α-helix	348-354	7
α-helix	365-379	15
α-helix	383-395	13
α-helix	399-412	14
β-strand	420-422	3	4
α-helix	423-424	2
α-helix	437-443	7
β-strand	455-457	3	4
α-helix	460-462	3
α-helix	463-480	18

Chain B: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	5
β-strand	11	1	6
β-strand	16-23	8	5
α-helix	28-31	4
β-strand	33-39	7	7
β-strand	45-51	7	7
β-strand	57-59	3	7
α-helix	61-63	3
β-strand	67-72	6	5
β-strand	77-85	9	5
α-helix	87-89	3
β-strand	91-98	8	7
β-strand	104	1	7
β-strand	112-114	3	7
β-strand	115	1	6

Chain C: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	8
β-strand	10-12	3	9
β-strand	18-25	8	8
α-helix	29-31	3
β-strand	34-39	6	9
β-strand	46-51	6	9
β-strand	58-60	3	9
β-strand	68-73	6	8
α-helix	74-76	3
β-strand	78-83	6	8
α-helix	88-90	3
β-strand	92-101	10	9
β-strand	109-113	5	9
β-strand	117-121	5	9

Chain D: 20 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	5-16	12
β-strand	23-24	2	10
β-strand	38-42	5	10
α-helix	43-45	3
α-helix	52-54	3
β-strand	55-60	6	10
α-helix	61-64	4
β-strand	65	1	11
α-helix	69-71	3
β-strand	75-81	7	10
β-strand	119-124	6	10
α-helix	129-136	8
β-strand	139	1	11
α-helix	145-153	9
β-strand	156-166	11	10
β-strand	170	1	12
β-strand	208	1	12
β-strand	213-222	10	10
β-strand	223	1	13
β-strand	228-230	3	10
β-strand	240	1	13
α-helix	286-300	15
α-helix	301-303	3
α-helix	306-319	14
α-helix	323-331	9
β-strand	341	1	14
α-helix	342-343	2
α-helix	348-354	7
β-strand	357	1	15
β-strand	362	1	14
β-strand	363	1	15
α-helix	365-380	16
α-helix	383-394	12
α-helix	399-412	14
β-strand	420-422	3	16
α-helix	425-427	3
α-helix	437-445	9
β-strand	455-457	3	16
α-helix	460-462	3
α-helix	463-479	17

Chain E: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	17
β-strand	11	1	18
β-strand	18-24	7	17
α-helix	28-31	4
β-strand	33-39	7	19
β-strand	46-51	6	19
β-strand	57-59	3	19
β-strand	67-72	6	17
β-strand	77-82	6	17
β-strand	91-98	8	19
β-strand	104	1	19
β-strand	112-114	3	19
β-strand	115	1	18

Chain F: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	20
β-strand	11-12	2	21
β-strand	16-25	10	20
α-helix	29-31	3
β-strand	34-39	6	22
β-strand	45-51	7	22
β-strand	58-60	3	22
β-strand	68-73	6	20
β-strand	78-86	9	20
α-helix	88-90	3
β-strand	92-102	11	22
β-strand	108-113	6	22
β-strand	117-119	3	22
β-strand	120-121	2	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gasdermin-D	A, D	protein	447	Homo sapiens	P57764 (AlphaFold model)
VHH-2	B, E	protein	132	Lama glama
VHH-6	C, F	protein	141	Lama glama

Sequence of entity 1 (A, D), FASTA

>7Z1X_1 Gasdermin-D (chains A, D)
MGSAFERVVRRVVQELDHGGEFIPVTSLQSSTGFQPYCLVVRKPSSSWFWKPRYKCVNLS
IKDILEPDAAEPDVQRGRSFHFYDAMDGQIQGSVELAAPGQAKIAGGAAVSDSSSTSMNV
YSLSVDPNTWQTLLHERHLRQPEHKVLQQLRSRGDNVYVVTEVLQTQKEVEVTRTHKREG
SGREGQGHLSQKKTVTIPSGSTLAFRVAQLVIDSDLDVLLFPDKKQRTFQPPATGLTDGV
PAEGAFTEDFQGLRAEVETISKELELLDRELCQLLLEGLEGVLRDQLALRALEEALEQGQ
SLGPVEPLDGPAGAVLECLVLSSGMLVPELAIPVVYLLGALTMLSETQHKLLAEALESQT
LLGPLELVGSLLEQSAPWQERSTMSLPPGLLGNSWGEGAPAWVLLDECGLELGEDTPHVC
WEPQAQGRMCALYASLALLSGLSQEPH

Sequence of entity 2 (B, E), FASTA

>7Z1X_2 VHH-2 (chains B, E)
QVQLVESGGGLVQPGGSLRLSCVDSRSWINVYGANWYRQAPGKERELVAALTSGGTTNYA
DSVKGRFTISRDNAKNTVYLQMRDLKPEDTAVYYCNLERYTGSSVYPWGQGTQVTVSSGG
LPETGGHHHHHH

Sequence of entity 3 (C, F), FASTA

>7Z1X_3 VHH-6 (chains C, F)
QVQLVETGGGLVQPGGSLRLSCTASGFIFSANQMNWVRQAPGKGLEWLSGISTRGDTTSY
ADSVKGRFTISRDNAKNTLYLQMNSLQPDDTAVYFCARVCIRGPEPKLRCDDWGQGTQVT
VSSGGYPYDVPDYAGHHHHHH

Primary citation

Pyroptosis inhibiting nanobodies block Gasdermin D pore formation. Kopp, A., Hagelueken, G., Jamitzky, I. et al. Nat Commun (2023) 14:7923-7923. DOI 10.1038/s41467-023-43707-z · 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
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
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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