Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 22.35 kDa 
• Atom Count: 1445 
• Modelled Residue Count: 192 
• Deposited Residue Count: 209 
• Unique protein chains: 1

6AO4

Crystal structure of the human gasdermin D C-terminal domain

• PDB DOI: 10.2210/pdb6AO4/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-08-15 Released: 2018-04-11 
• Deposition Author(s): Liu, Z., Wang, C., Yang, J., Xiao, T.S.
• Funding Organization(s): National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.290 
• R-Value Work: 0.232 
• R-Value Observed: 0.236 

Literature

Structures of the Gasdermin D C-Terminal Domains Reveal Mechanisms of Autoinhibition.

Liu, Z., Wang, C., Rathkey, J.K., Yang, J., Dubyak, G.R., Abbott, D.W., Xiao, T.S.

(2018) Structure 26: 778-784.e3

• PubMed: 29576317 
• DOI: 10.1016/j.str.2018.03.002
• Primary Citation of Related Structures:  
  6AO3, 6AO4


• PubMed Abstract: 
  

Pyroptosis is an inflammatory form of programmed cell death that plays important roles in immune protection against infections and in inflammatory disorders. Gasdermin D (GSDMD) is an executor of pyroptosis upon cleavage by caspases-1/4/5/11 following canonical and noncanonical inflammasome activation. GSDMD N-terminal domain assembles membrane pores to induce cytolysis, whereas its C-terminal domain inhibits cell death through intramolecular association with the N domain. The molecular mechanisms of autoinhibition for GSDMD are poorly characterized. Here we report the crystal structures of the human and murine GSDMD C-terminal domains, which differ from those of the full-length murine GSDMA3 and the human GSDMB C-terminal domain. Mutations of GSDMD C-domain residues predicted to locate at its interface with the N-domain enhanced pyroptosis. Our results suggest that GSDMDs may employ a distinct mode of intramolecular domain interaction and autoinhibition, which may be relevant to its unique role in pyroptosis downstream of inflammasome activation.

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Organizational Affiliation: 

Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA; Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, OH 44106, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gasdermin-D	A	209	Homo sapiens	Mutation(s): 0  Gene Names: GSDMD, DFNA5L, GSDMDC1, FKSG10
UniProt & NIH Common Fund Data Resources
Find proteins for P57764 (Homo sapiens) Explore P57764  Go to UniProtKB:  P57764
PHAROS:  P57764

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.290 
• R-Value Work: 0.232 
• R-Value Observed: 0.236 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.75	α = 90
b = 108.54	β = 90
c = 45.91	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-08-15 
• Released Date: 2018-04-11 
Deposition Author(s): Liu, Z., Wang, C., Yang, J., Xiao, T.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)	United States	AR069908

Revision History  

• Version 1.0: 2018-04-11
  Type: Initial release
  
• Version 1.1: 2018-05-09
  Changes: Data collection, Database references
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence