7N51 | pdb_00007n51

Structure of a bacterial gasdermin from Vitiosangium sp.

• PDB DOI: https://doi.org/10.2210/pdb7N51/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Vitiosangium sp. GDMCC 1.1324
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-06-04 Released: 2021-06-16 
• Deposition Author(s): Johnson, A.G., Kranzusch, P.J.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 
  0.218 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

Bacterial gasdermins reveal an ancient mechanism of cell death.

Johnson, A.G., Wein, T., Mayer, M.L., Duncan-Lowey, B., Yirmiya, E., Oppenheimer-Shaanan, Y., Amitai, G., Sorek, R., Kranzusch, P.J.

(2022) Science 375: 221-225

• PubMed: 35025633 
• DOI: https://doi.org/10.1126/science.abj8432
• Primary Citation Related Structures: 
  7N50, 7N51, 7N52


• PubMed Abstract: 
  

  Gasdermin proteins form large membrane pores in human cells that release immune cytokines and induce lytic cell death. Gasdermin pore formation is triggered by caspase-mediated cleavage during inflammasome signaling and is critical for defense against pathogens and cancer. We discovered gasdermin homologs encoded in bacteria that defended against phages and executed cell death. Structures of bacterial gasdermins revealed a conserved pore-forming domain that was stabilized in the inactive state with a buried lipid modification. Bacterial gasdermins were activated by dedicated caspase-like proteases that catalyzed site-specific cleavage and the removal of an inhibitory C-terminal peptide. Release of autoinhibition induced the assembly of large and heterogeneous pores that disrupted membrane integrity. Thus, pyroptosis is an ancient form of regulated cell death shared between bacteria and animals.

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Organizational Affiliation: 
• Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
Harvard Center for Cryo-Electron Microscopy, Harvard Medical School, Boston, MA 02115, USA.
Parker Institute for Cancer Immunotherapy, Dana-Farber Cancer Institute, Boston, MA 02115, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 28.49 kDa 
• Atom Count: 2,134 
• Modeled Residue Count: 263 
• Deposited Residue Count: 266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gasdermin	A	266	Vitiosangium sp. GDMCC 1.1324	Mutation(s): 0  Gene Names: DAT35_31115
UniProt
Find proteins for A0A2T4VDM4 (Vitiosangium sp. (strain GDMCC 1.1324)) Explore A0A2T4VDM4  Go to UniProtKB:  A0A2T4VDM4

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
P1L	A	L-PEPTIDE LINKING	C19 H37 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free:  0.218 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.383	α = 90
b = 87.383	β = 90
c = 141.969	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-06-16 
Deposition Author(s): Johnson, A.G., Kranzusch, P.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	T32CA207021

Revision History  

• Version 1.0: 2021-06-16
  Type: Initial release
  
• Version 1.1: 2022-01-26
  Changes: Database references