8EFP: GSDMB

CryoEM structure of GSDMB in complex with shigella IpaH7.8. Determined by electron microscopy at 3.8 Å resolution. Released 29 Mar 2023.

Method: Electron microscopy
Resolution: 3.8 Å
Organisms: Shigella flexneri, Homo sapiens
Chains: 2
Atoms: 4,705
Mol. weight: 112.01 kDa
Released: 29 Mar 2023

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

Secondary structure: helices and β-sheets

8EFP contains 23 α-helices and 19 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 B: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	23-36	14
α-helix	44-55	12
α-helix	74-76	3
β-strand	82-83	2	1
α-helix	91-92	2
β-strand	101-103	3	1
α-helix	111-116	6
β-strand	121-123	3	1
β-strand	141-143	3	1
β-strand	147	1	2
α-helix	154-156	3
β-strand	161-163	3	1
β-strand	167	1	2
β-strand	181-183	3	1
β-strand	204-207	4	1
α-helix	218-221	4
β-strand	227-230	4	1
α-helix	238-248	11

Chain C: 15 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	4-17	14
β-strand	22-24	3	3
α-helix	58-61	4
α-helix	69-76	8
β-strand	82-86	5	3
β-strand	118-124	7	3
α-helix	127-135	9
α-helix	144-149	6
β-strand	157-164	8	3
β-strand	172	1	4
α-helix	181-185	5
β-strand	195	1	4
β-strand	206-210	5	3
α-helix	249-261	13
α-helix	265-278	14
α-helix	282-298	17
α-helix	308-314	7
β-strand	315	1	5
β-strand	321	1	5
α-helix	323-338	16
α-helix	343-352	10
α-helix	355-368	14
α-helix	372-375	4
α-helix	384-403	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Probable E3 ubiquitin-protein ligase ipaH7.8	B	protein	565	Shigella flexneri	P18014 (AlphaFold model)
Gasdermin-B	C	protein	416	Homo sapiens	Q8TAX9 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>8EFP_1 Probable E3 ubiquitin-protein ligase ipaH7.8 (chains B)
MFSVNNTHSSVSCSPSINSNSTSNEHYLRILTEWEKNSSPGEERGIAFNRLSQCFQNQEA
VLNLSDLNLTSLPELPKHISALIVENNKLTSLPKLPAFLKELNADNNRLSVIPELPESLT
TLSVRSNQLENLPVLPNHLTSLFVENNRLYNLPALPEKLKFLHVYYNRLTTLPDLPDKLE
ILCAQRNNLVTFPQFSDRNNIRQKEYYFHFNQITTLPESFSQLDSSYRINISGNPLSTRV
LQSLQRLTSSPDYHGPQIYFSMSDGQQNTLHRPLADAVTAWFPENKQSDVSQIWHAFEHE
EHANTFSAFLDRLSDTVSARNTSGFREQVAAWLEKLSASAELRQQSFAVAADATESCEDR
VALTWNNLRKTLLVHQASEGLFDNDTGALLSLGREMFRLEILEDIARDKVRTLHFVDEIE
VYLAFQTMLAEKLQLSTAVKEMRFYGVSGVTANDLRTAEAMVRSREENEFTDWFSLWGPW
HAVLKRTEADRWAQAEEQKYEMLENEYSQRVADRLKASGLSGDADAEREAGAQVMRETEQ
QIYRQLTDEVLALRLSENGSRLHHS

Sequence of entity 2 (C), FASTA

>8EFP_2 Gasdermin-B (chains C)
MFSVFEEITRIVVKEMDAGGDMIAVRSLVDADRFRCFHLVGEKRTFFGCRHYTTGLTLMD
ILDTDGDKWLDELDSGLQGQKAEFQILDNVDSTGELIVRLPKEITISGSFQGFHHQKIKI
SENRISQQYLATLENRKLKRELPFSFRSINTRENLYLVTETLETVKEETLKSDRQYKFWS
QISQGHLSYKHKGQREVTIPPNRVLSYRVKQLVFPNKETMNIHFRGKTKSFPEEKDGASS
CLGKSLGSEDSRNMKEKLEDMESVLKDLTEEKRKDVLNSLAKCLGKEDIRQDLEQRVSEV
LISGELHMEDPDKPLLSSLFNAAGVLVEARAKAILDFLDALLELSEEQQFVAEALEKGTL
PLLKDQVKSVMEQNWDELASSPPDMDYDPEARILCALYVVVSILLELAEGPTSVSS

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 P18014 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3CKD 2.65 Å, Crystal structure of the C-terminal domain of the Shigella type III effector IpaH
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
8GTK 3.1 Å, Crystal structure of IpaH7.8-LRR and GSDMB isoform-1 complex

Browse structure collections

About this viewer

MolViewer shows 8EFP directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.