8GTK | pdb_00008gtk

Crystal structure of IpaH7.8-LRR and GSDMB isoform-1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.290 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.266 (Depositor), 0.266 (DCC) 
  • R-Value Observed: 
    0.268 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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: 72.84 kDa 
  • Atom Count: 4,528 
  • Modeled Residue Count: 560 
  • Deposited Residue Count: 638 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GSDMB isoform-1397Homo sapiensMutation(s): 0 
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
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable E3 ubiquitin-protein ligase ipaH7.8241Shigella 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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.290 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.266 (Depositor), 0.266 (DCC) 
  • R-Value Observed: 0.268 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.732α = 90
b = 102.732β = 90
c = 121.316γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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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