8GTN: Gasdermin B pore

Cryo-EM structure of the gasdermin B pore. Determined by electron microscopy at 3.17 Å resolution. Released 12 Apr 2023.

Method: Electron microscopy
Resolution: 3.17 Å
Organism: Homo sapiens
Chains: 27
Atoms: 48,303
Mol. weight: 772.98 kDa
Released: 12 Apr 2023

Explore 8GTN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8GTN contains 135 α-helices and 324 β-strands across 27 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.

Chains A, AA, B, BA, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, V, W, X, Y and Z: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	4-16	13
β-strand	23-24	2	1
α-helix	32-34	3
β-strand	38-44	7	1
β-strand	49-57	9	1
α-helix	58-61	4
β-strand	82-100	19	1
β-strand	104-124	21	1
α-helix	127-132	6
β-strand	136	1	2
α-helix	144-147	4
β-strand	155-164	10	1
β-strand	168-181	14	1
β-strand	186-199	14	1
β-strand	204-213	10	1
β-strand	220	1	2
β-strand	221-223	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 4 of Gasdermin-B	A, AA, B, BA, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, V, W, X, Y, Z	protein	246	Homo sapiens	Q8TAX9 (AlphaFold model)

Sequence of entity 1 (A, AA, B, BA, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, V, W, X, Y, Z), FASTA

>8GTN_1 Isoform 4 of Gasdermin-B (chains A, AA, B, BA, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, V, W, X, Y, Z)
SGRPMFSVFEEITRIVVKEMDAGGDMIAVRSLVDADRFRCFHLVGEKRTFFGCRHYTTGL
TLMDILDTDGDKWLDELDSGLQGQKAEFQILDNVDSTGELIVRLPKEITISGSFQGFHHQ
KIKISENRISQQYLATLENRKLKRELPFSFRSINTRENLYLVTETLETVKEETLKSDRQY
KFWSQISQGHLSYKHKGQREVTIPPNRVLSYRVKQLVFPNKETMNIHFRGKTKSFPEGKS
LEVLFQ

Primary citation

Structural mechanisms for regulation of GSDMB pore-forming activity. Zhong, X., Zeng, H., Zhou, Z. et al. Nature (2023) 616:598-605. DOI 10.1038/s41586-023-05872-5 · PubMed

Other PDB entries of the same protein (UniProt Q8TAX9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5TIB 2.6 Å, Gasdermin-B C-terminal domain containing the polymorphism residues Arg299:Ser306 fused…
9K1S 2.69 Å, Crystal structure of human granzyme A in complex with GSDMB-C domain
7WJQ 2.7 Å, Crystal structure of GSDMB in complex with Ipah7.8
8GTJ 2.7 Å, Crystal structure of IpaH7.8-LRR and GSDMB isoform-4 complex
5TJ2 2.8 Å, Gasdermin-B C-terminal domain containing the polymorphism residues Gly299:Ser306 fused…
8GTK 3.1 Å, Crystal structure of IpaH7.8-LRR and GSDMB isoform-1 complex
9XSG 3.4 Å, CryoEM structure of hGZMA-hGSDMB
5TJ4 3.5 Å, Gasdermin-B C-terminal domain containing the polymorphism residues Gly299:Pro306 fused…
21AM 3.59 Å, CryoEM structure of hGZMA-hGSDMBctd
8EFP 3.8 Å, CryoEM structure of GSDMB in complex with shigella IpaH7.8
8ET1 4.48 Å, CryoEM structure of GSDMB pore without transmembrane beta-barrel
8ET2 4.96 Å, CryoEM structure of the GSDMB pore

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