8ET2: GSDMB pore

CryoEM structure of the GSDMB pore. Determined by electron microscopy at 4.96 Å resolution. Released 29 Mar 2023.

Method: Electron microscopy
Resolution: 4.96 Å
Organism: Homo sapiens
Chains: 24
Atoms: 43,584
Mol. weight: 1124.36 kDa
Released: 29 Mar 2023

Explore 8ET2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ET2 contains 72 α-helices and 360 β-strands across 24 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, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W and X: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	5-16	12
β-strand	23-24	2	1
β-strand	43-44	2	2
β-strand	50-51	2	2
β-strand	84-95	12	3
β-strand	98-99	2	4
β-strand	105-106	2	4
β-strand	109-120	12	3
β-strand	121-123	3	5
α-helix	128-134	7
α-helix	145-151	7
β-strand	156	1	6
β-strand	161-163	3	5
β-strand	170-180	11	3
β-strand	187-197	11	3
β-strand	206-207	2	1
β-strand	211-213	3	6
β-strand	220-222	3	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 1 of Gasdermin-B	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	protein	411	Homo sapiens	Q8TAX9 (AlphaFold model)

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

>8ET2_1 Isoform 1 of Gasdermin-B (chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X)
MFSVFEEITRIVVKEMDAGGDMIAVRSLVDADRFRCFHLVGEKRTFFGCRHYTTGLTLMD
ILDTDGDKWLDELDSGLQGQKAEFQILDNVDSTGELIVRLPKEITISGSFQGFHHQKIKI
SENRISQQYLATLENRKLKRELPFSFRSINTRENLYLVTETLETVKEETLKSDRQYKFWS
QISQGHLSYKHKGQREVTIPPNRVLSYRVKQLVFPNKETMSAGLDIHFRGKTKSFPEGKS
LGSEDSRNMKEKLEDMESVLKDLTEEKRKDVLNSLAKCLGKEDIRQDLEQRVSEVLISGE
LHMEDPDKPLLSSLFNAAGVLVEARAKAILDFLDALLELSEEQQFVAEALEKGTLPLLKD
QVKSVMEQNWDELASSPPDMDYDPEARILCALYVVVSILLELAEGPTSVSS

Primary citation

Structural basis for GSDMB pore formation and its targeting by IpaH7.8. Wang, C., Shivcharan, S., Tian, T. et al. Nature (2023) 616:590-597. DOI 10.1038/s41586-023-05832-z · 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
8GTN 3.17 Å, Cryo-EM structure of the gasdermin B pore
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

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