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- PDB-8et1: CryoEM structure of GSDMB pore without transmembrane beta-barrel -

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Basic information

Entry
Database: PDB / ID: 8et1
TitleCryoEM structure of GSDMB pore without transmembrane beta-barrel
ComponentsIsoform 1 of Gasdermin-B
KeywordsIMMUNE SYSTEM / Pore-forming protein / GSDMB / pyroptosis
Function / homology
Function and homology information


cytotoxic T cell pyroptotic process / wide pore channel activity / killing by host of symbiont cells / cardiolipin binding / phosphatidylinositol-4-phosphate binding / phosphatidylserine binding / pyroptosis / phosphatidylinositol-4,5-bisphosphate binding / phospholipid binding / killing of cells of another organism ...cytotoxic T cell pyroptotic process / wide pore channel activity / killing by host of symbiont cells / cardiolipin binding / phosphatidylinositol-4-phosphate binding / phosphatidylserine binding / pyroptosis / phosphatidylinositol-4,5-bisphosphate binding / phospholipid binding / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to bacterium / plasma membrane / cytoplasm
Similarity search - Function
Gasdermin, pore forming domain / Gasdermin pore forming domain / Gasdermin, PUB domain / Gasdermin PUB domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.48 Å
AuthorsWang, C. / Ruan, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nature / Year: 2023
Title: Structural basis for GSDMB pore formation and its targeting by IpaH7.8.
Authors: Chengliang Wang / Sonia Shivcharan / Tian Tian / Skylar Wright / Danyang Ma / JengYih Chang / Kunpeng Li / Kangkang Song / Chen Xu / Vijay A Rathinam / Jianbin Ruan /
Abstract: Gasdermins (GSDMs) are pore-forming proteins that play critical roles in host defence through pyroptosis. Among GSDMs, GSDMB is unique owing to its distinct lipid-binding profile and a lack of ...Gasdermins (GSDMs) are pore-forming proteins that play critical roles in host defence through pyroptosis. Among GSDMs, GSDMB is unique owing to its distinct lipid-binding profile and a lack of consensus on its pyroptotic potential. Recently, GSDMB was shown to exhibit direct bactericidal activity through its pore-forming activity. Shigella, an intracellular, human-adapted enteropathogen, evades this GSDMB-mediated host defence by secreting IpaH7.8, a virulence effector that triggers ubiquitination-dependent proteasomal degradation of GSDMB. Here, we report the cryogenic electron microscopy structures of human GSDMB in complex with Shigella IpaH7.8 and the GSDMB pore. The structure of the GSDMB-IpaH7.8 complex identifies a motif of three negatively charged residues in GSDMB as the structural determinant recognized by IpaH7.8. Human, but not mouse, GSDMD contains this conserved motif, explaining the species specificity of IpaH7.8. The GSDMB pore structure shows the alternative splicing-regulated interdomain linker in GSDMB as a regulator of GSDMB pore formation. GSDMB isoforms with a canonical interdomain linker exhibit normal pyroptotic activity whereas other isoforms exhibit attenuated or no pyroptotic activity. Overall, this work sheds light on the molecular mechanisms of Shigella IpaH7.8 recognition and targeting of GSDMs and shows a structural determinant in GSDMB critical for its pyroptotic activity.
History
DepositionOct 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 3, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 1 of Gasdermin-B
B: Isoform 1 of Gasdermin-B
C: Isoform 1 of Gasdermin-B
D: Isoform 1 of Gasdermin-B
E: Isoform 1 of Gasdermin-B
F: Isoform 1 of Gasdermin-B
G: Isoform 1 of Gasdermin-B
H: Isoform 1 of Gasdermin-B
I: Isoform 1 of Gasdermin-B
J: Isoform 1 of Gasdermin-B
K: Isoform 1 of Gasdermin-B
L: Isoform 1 of Gasdermin-B
M: Isoform 1 of Gasdermin-B
N: Isoform 1 of Gasdermin-B
O: Isoform 1 of Gasdermin-B
P: Isoform 1 of Gasdermin-B
Q: Isoform 1 of Gasdermin-B
R: Isoform 1 of Gasdermin-B
S: Isoform 1 of Gasdermin-B
T: Isoform 1 of Gasdermin-B
U: Isoform 1 of Gasdermin-B
V: Isoform 1 of Gasdermin-B
W: Isoform 1 of Gasdermin-B
X: Isoform 1 of Gasdermin-B


Theoretical massNumber of molelcules
Total (without water)1,124,35824
Polymers1,124,35824
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Isoform 1 of Gasdermin-B / Gasdermin-like protein


Mass: 46848.250 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSDMB, GSDML, PP4052, PRO2521 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TAX9

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: GSDMB-pore / Type: COMPLEX / Details: C24 symmetry / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: DIFFRACTION / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM softwareName: SerialEM / Category: image acquisition
CTF correctionType: NONE
3D reconstructionResolution: 4.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41799 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00336528
ELECTRON MICROSCOPYf_angle_d0.7548960
ELECTRON MICROSCOPYf_dihedral_angle_d6.4664752
ELECTRON MICROSCOPYf_chiral_restr0.0465496
ELECTRON MICROSCOPYf_plane_restr0.0056240

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