8GTJ

Crystal structure of IpaH7.8-LRR and GSDMB isoform-4 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.242 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural mechanisms for regulation of GSDMB pore-forming activity.

Zhong, X.Zeng, H.Zhou, Z.Su, Y.Cheng, H.Hou, Y.She, Y.Feng, N.Wang, J.Shao, F.Ding, J.

(2023) Nature 616: 598-605

  • DOI: https://doi.org/10.1038/s41586-023-05872-5
  • Primary Citation of Related Structures:  
    8GTJ, 8GTK, 8GTN

  • PubMed Abstract: 

    Cytotoxic lymphocyte-derived granzyme A (GZMA) cleaves GSDMB, a gasdermin-family pore-forming protein 1,2 , to trigger target cell pyroptosis 3 . GSDMB and the charter gasdermin family member GSDMD 4,5 have been inconsistently reported to be degraded by the Shigella flexneri ubiquitin-ligase virulence factor IpaH7.8 (refs. 6,7 ). Whether and how IpaH7.8 targets both gasdermins is undefined, and the pyroptosis function of GSDMB has even been questioned recently 6,8 . Here we report the crystal structure of the IpaH7.8-GSDMB complex, which shows how IpaH7.8 recognizes the GSDMB pore-forming domain. We clarify that IpaH7.8 targets human (but not mouse) GSDMD through a similar mechanism. The structure of full-length GSDMB suggests stronger autoinhibition than in other gasdermins 9,10 . GSDMB has multiple splicing isoforms that are equally targeted by IpaH7.8 but exhibit contrasting pyroptotic activities. Presence of exon 6 in the isoforms dictates the pore-forming, pyroptotic activity in GSDMB. We determine the cryo-electron microscopy structure of the 27-fold-symmetric GSDMB pore and depict conformational changes that drive pore formation. The structure uncovers an essential role for exon-6-derived elements in pore assembly, explaining pyroptosis deficiency in the non-canonical splicing isoform used in recent studies 6,8 . Different cancer cell lines have markedly different isoform compositions, correlating with the onset and extent of pyroptosis following GZMA stimulation. Our study illustrates fine regulation of GSDMB pore-forming activity by pathogenic bacteria and mRNA splicing and defines the underlying structural mechanisms.


  • Organizational Affiliation

    Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing, PR China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 4 of Gasdermin-B
A, C
414Homo sapiensMutation(s): 0 
Gene Names: GSDMBGSDMLPP4052PRO2521
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TAX9 (Homo sapiens)
Explore Q8TAX9 
Go to UniProtKB:  Q8TAX9
PHAROS:  Q8TAX9
GTEx:  ENSG00000073605 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TAX9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Probable E3 ubiquitin-protein ligase ipaH7.8
B, D
241Shigella flexneriMutation(s): 0 
Gene Names: ipaH7.8CP0078pWR501_0084SFLP133
EC: 2.3.2.27
UniProt
Find proteins for P18014 (Shigella flexneri)
Explore P18014 
Go to UniProtKB:  P18014
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18014
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.242 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.338α = 90
b = 88.338β = 90
c = 335.624γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChina--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-12
    Type: Initial release
  • Version 1.1: 2023-05-03
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description