6CB8

Cryo-EM structure of the Gasdermin A3 membrane pore

  • Classification: IMMUNE SYSTEM
  • Organism(s): Mus musculus
  • Expression System: Escherichia coli
  • Mutation(s): No 
  • Membrane Protein: Yes  OPMPDBTMmpstruc

  • Deposited: 2018-02-02 Released: 2018-04-25 
  • Deposition Author(s): Ruan, J., Wu, H.
  • Funding Organization(s): National Institutes of Health/National Institute on Minority Health and Health Disparities (NIH/NIMHD), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Cryo-EM structure of the gasdermin A3 membrane pore.

Ruan, J.Xia, S.Liu, X.Lieberman, J.Wu, H.

(2018) Nature 557: 62-67

  • DOI: https://doi.org/10.1038/s41586-018-0058-6
  • Primary Citation of Related Structures:  
    6CB8

  • PubMed Abstract: 

    Gasdermins mediate inflammatory cell death after cleavage by caspases or other, unknown enzymes. The cleaved N-terminal fragments bind to acidic membrane lipids to form pores, but the mechanism of pore formation remains unresolved. Here we present the cryo-electron microscopy structures of the 27-fold and 28-fold single-ring pores formed by the N-terminal fragment of mouse GSDMA3 (GSDMA3-NT) at 3.8 and 4.2 Å resolutions, and of a double-ring pore at 4.6 Å resolution. In the 27-fold pore, a 108-stranded anti-parallel β-barrel is formed by two β-hairpins from each subunit capped by a globular domain. We identify a positively charged helix that interacts with the acidic lipid cardiolipin. GSDMA3-NT undergoes radical conformational changes upon membrane insertion to form long, membrane-spanning β-strands. We also observe an unexpected additional symmetric ring of GSDMA3-NT subunits that does not insert into the membrane in the double-ring pore, which may represent a pre-pore state of GSDMA3-NT. These structures provide a basis that explains the activities of several mutant gasdermins, including defective mutants that are associated with cancer.


  • Organizational Affiliation

    Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gasdermin-A3269Mus musculusMutation(s): 0 
Gene Names: Gsdma3Gsdm3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q5Y4Y6 (Mus musculus)
Explore Q5Y4Y6 
Go to UniProtKB:  Q5Y4Y6
IMPC:  MGI:3044668
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5Y4Y6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download Ideal Coordinates CCD File 
B [auth A]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Minority Health and Health Disparities (NIH/NIMHD)United StatesDP1HD087988
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01Al124491
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI123265

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2018-05-09
    Changes: Data collection, Database references
  • Version 1.2: 2018-05-16
    Changes: Data collection, Database references
  • Version 1.3: 2018-10-03
    Changes: Data collection, Refinement description
  • Version 1.4: 2019-12-18
    Changes: Author supporting evidence, Other
  • Version 1.5: 2024-03-13
    Changes: Data collection, Database references, Derived calculations