8GTK: IpaH7.8-LRR and GSDMB isoform-1 complex

Crystal structure of IpaH7.8-LRR and GSDMB isoform-1 complex. Determined by X-ray diffraction at 3.1 Å resolution. Released 12 Apr 2023.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: Homo sapiens, Shigella flexneri
Chains: 2
Atoms: 4,528
Mol. weight: 72.84 kDa
Released: 12 Apr 2023

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

Secondary structure: helices and β-sheets

8GTK contains 25 α-helices and 28 β-strands across 2 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: 14 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	4-17	14
β-strand	23-24	2	1
α-helix	32-34	3
β-strand	38	1	2
β-strand	39	1	1
β-strand	40-43	4	2
β-strand	50-57	8	2
α-helix	58-61	4
β-strand	62	1	3
α-helix	71-76	6
β-strand	77-86	10	1
β-strand	91-93	3	4
β-strand	104-112	9	1
α-helix	114-121	8
β-strand	125	1	3
α-helix	131-134	4
β-strand	144-151	8	1
β-strand	155-159	5	4
β-strand	182-186	5	4
β-strand	191-197	7	1
α-helix	228-240	13
α-helix	244-256	13
α-helix	261-277	17
α-helix	287-293	7
β-strand	294	1	5
β-strand	300	1	5
α-helix	302-315	14
α-helix	322-329	8
α-helix	334-348	15
α-helix	363-381	19

Chain B: 11 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	28-36	9
α-helix	44-56	13
β-strand	61-63	3	6
α-helix	73-76	4
β-strand	81-83	3	6
β-strand	91	1	7
α-helix	93-95	3
β-strand	101-103	3	6
β-strand	111	1	7
α-helix	113-116	4
β-strand	121-123	3	6
α-helix	133-136	4
β-strand	141-143	3	6
α-helix	154-156	3
β-strand	161-163	3	6
α-helix	172-175	4
β-strand	181-183	3	6
α-helix	192-194	3
β-strand	204-207	4	6
α-helix	218-222	5
β-strand	227-230	4	6
α-helix	238-247	10
β-strand	257-259	3	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GSDMB isoform-1	A	protein	397	Homo sapiens	Q8TAX9 (AlphaFold model)
Probable E3 ubiquitin-protein ligase ipaH7.8	B	protein	241	Shigella flexneri	P18014 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8GTK_1 GSDMB isoform-1 (chains A)
GPGSGRPMFSVFEEITRIVVKEMDAGGDMIAVRSLVDADRFRCFHLVGEKRTFFGCRHYT
TGLTLMDILDTDGDKAEFQILDNVDSTGELIVRLPKEITISGSFQGFHHQKIKISENRIS
QQYLATLENRKLKRELPFSFRSINTRENLYLVTETLETVKEETLKSDRQYKFWSQISQGH
LSYKHKGQREVTIPPNRVLSYRVKQLVFPNKETMKKDGASSCLGKSLGSEDSRNMKEKLE
DMESVLKDLTEEKRKDVLNSLAKCLGKEDIRQDLEQRVSEVLISGELHMEDPDKPLLSSL
FNAAGVLVEARAKAILDFLDALLELSEEQQFVAEALEKGTLPLLKDQVKSVMEQNWDELA
SSPPDMDYDPEARILCALYVVVSILLELAEGPTSVSS

Sequence of entity 2 (B), FASTA

>8GTK_2 Probable E3 ubiquitin-protein ligase ipaH7.8 (chains B)
MSNEHYLRILTEWEKNSSPGEERGIAFNRLSQCFQNQEAVLNLSDLNLTSLPELPKHISA
LIVENNKLTSLPKLPAFLKELNADNNRLSVIPELPESLTTLSVRSNQLENLPVLPNHLTS
LFVENNRLYNLPALPEKLKFLHVYYNRLTTLPDLPDKLEILCAQRNNLVTFPQFSDRNNI
RQKEYYFHFNQITTLPESFSQLDSSYRINISGNPLSTRVLQSLQRLTSSPDYHGPQIYFS
M

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…
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
8ET2 4.96 Å, CryoEM structure of the GSDMB pore

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