8GTN | pdb_00008gtn

Cryo-EM structure of the gasdermin B pore


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.17 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8GTN

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 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.

Macromolecule Content 

  • Total Structure Weight: 772.98 kDa 
  • Atom Count: 48,303 
  • Modeled Residue Count: 5,859 
  • Deposited Residue Count: 6,642 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform 4 of Gasdermin-B246Homo 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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.17 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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: 2024-07-03
    Changes: Data collection