8GTJ: IpaH7.8-LRR and GSDMB isoform-4 complex

Crystal structure of IpaH7.8-LRR and GSDMB isoform-4 complex. Determined by X-ray diffraction at 2.7 Å resolution. Released 12 Apr 2023.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Homo sapiens, Shigella flexneri
Chains: 4
Atoms: 9,607
Mol. weight: 149.94 kDa
Released: 12 Apr 2023

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

Secondary structure: helices and β-sheets

8GTJ contains 53 α-helices and 56 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, 18 β-strands

Element	Residues	Length	Sheet
α-helix	3-17	15
β-strand	23-24	2	1
α-helix	28-30	3
β-strand	38-44	7	1
β-strand	49-57	9	1
β-strand	62	1	2
α-helix	85-88	4
β-strand	90-99	10	1
β-strand	104-106	3	3
β-strand	117-125	9	1
α-helix	127-131	5
β-strand	136-137	2	4
β-strand	138	1	2
α-helix	139	1
α-helix	144-147	4
β-strand	154-164	11	1
β-strand	168-172	5	3
α-helix	177-179	3
β-strand	195-199	5	3
α-helix	200	1
β-strand	204-213	10	1
β-strand	219-220	2	4
β-strand	221-223	3	1
β-strand	236	1	5
α-helix	245-257	13
α-helix	261-272	12
α-helix	278-294	17
α-helix	304-309	6
β-strand	311	1	6
β-strand	317	1	6
α-helix	319-331	13
α-helix	332-334	3
α-helix	339-348	10
α-helix	351-365	15
α-helix	369-371	3
α-helix	372-373	2
α-helix	380-397	18

Chain B: 11 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	28-35	8
α-helix	44-57	14
β-strand	61-63	3	7
α-helix	75-76	2
β-strand	81-83	3	7
α-helix	94-96	3
β-strand	101-103	3	7
α-helix	114-116	3
β-strand	121-123	3	7
α-helix	134-136	3
β-strand	141-143	3	7
α-helix	154-156	3
β-strand	161-163	3	7
α-helix	173-176	4
β-strand	181-183	3	7
α-helix	192-194	3
β-strand	204-207	4	7
β-strand	217	1	8
α-helix	218-222	5
β-strand	227-230	4	7
α-helix	238-249	12
β-strand	257-259	3	7

Chain C: 14 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	4-17	14
β-strand	23-24	2	9
α-helix	30-32	3
β-strand	38-45	8	9
β-strand	48-57	10	9
β-strand	62	1	10
β-strand	90-99	10	9
β-strand	104-106	3	11
α-helix	115-116	2
β-strand	117-125	9	9
α-helix	127-131	5
β-strand	136-137	2	12
β-strand	138	1	10
α-helix	139	1
α-helix	144-147	4
β-strand	154-164	11	9
β-strand	168-172	5	11
α-helix	177-182	6
β-strand	196-199	4	11
β-strand	204-213	10	9
β-strand	219-220	2	12
β-strand	221-223	3	9
β-strand	236	1	8
α-helix	245-258	14
α-helix	261-274	14
α-helix	278-293	16
α-helix	323-333	11
α-helix	339-347	9
α-helix	351-361	11
α-helix	380-398	19

Chain D: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	28-36	9
α-helix	44-57	14
β-strand	61-63	3	13
α-helix	74-76	3
β-strand	81-83	3	13
α-helix	94-96	3
β-strand	101-103	3	13
β-strand	121-123	3	13
α-helix	134-136	3
β-strand	141-143	3	13
α-helix	154-156	3
β-strand	161-163	3	13
α-helix	173-176	4
β-strand	181-183	3	13
β-strand	204-207	4	13
β-strand	217	1	5
α-helix	218-222	5
β-strand	227-230	4	13
α-helix	238-249	12
β-strand	257-259	3	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 4 of Gasdermin-B	A, C	protein	414	Homo sapiens	Q8TAX9 (AlphaFold model)
Probable E3 ubiquitin-protein ligase ipaH7.8	B, D	protein	241	Shigella flexneri	P18014 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>8GTJ_1 Isoform 4 of Gasdermin-B (chains A, C)
GPGSGRPMFSVFEEITRIVVKEMDAGGDMIAVRSLVDADRFRCFHLVGEKRTFFGCRHYT
TGLTLMDILDTDGDKWLDELDSGLQGQKAEFQILDNVDSTGELIVRLPKEITISGSFQGF
HHQKIKISENRISQQYLATLENRKLKRELPFSFRSINTRENLYLVTETLETVKEETLKSD
RQYKFWSQISQGHLSYKHKGQREVTIPPNRVLSYRVKQLVFPNKETMNIHFRGKTKSFPE
GKSLGSEDSRNMKEKLEDMESVLKDLTEEKRKDVLNSLAKCLGKEDIRQDLEQRVSEVLI
SGELHMEDPDKPLLSSLFNAAGVLVEARAKAILDFLDALLELSEEQQFVAEALEKGTLPL
LKDQVKSVMEQNWDELASSPPDMDYDPEARILCALYVVVSILLELAEGPTSVSS

Sequence of entity 2 (B, D), FASTA

>8GTJ_2 Probable E3 ubiquitin-protein ligase ipaH7.8 (chains B, D)
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
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
8ET2 4.96 Å, CryoEM structure of the GSDMB pore

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