7N50 | pdb_00007n50

Structure of a bacterial gasdermin from Bradyrhizobium tropiciagri

PDB DOI: https://doi.org/10.2210/pdb7N50/pdb

Classification: IMMUNE SYSTEM
Organism(s): Bradyrhizobium tropiciagri
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-06-04 Released: 2021-06-23
Deposition Author(s): Johnson, A.G., Kranzusch, P.J.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.220 (Depositor), 0.220 (DCC)
R-Value Work:
0.188 (Depositor), 0.190 (DCC)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/science.abj8432
Primary Citation of 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.

Organizational Affiliation

Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.

Macromolecule Content

Total Structure Weight: 27.82 kDa
Atom Count: 1,990
Modelled Residue Count: 240
Deposited Residue Count: 259
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gasdermin	A	259	Bradyrhizobium tropiciagri	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.220 (Depositor), 0.220 (DCC)
R-Value Work: 0.188 (Depositor), 0.190 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.77	α = 90
b = 146.18	β = 90
c = 34.98	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-06-23

Deposition Author(s):

Kranzusch, P.J.

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

Revision History (Full details and data files)

Version 1.0: 2021-06-23
Type: Initial release
Version 1.1: 2022-01-26
Changes: Database references

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.