6VFE

Gasdermin D pore

• PDB DOI:  https://doi.org/10.2210/pdb6VFE/pdb
• EM Map EMD-21160: EMDB EMDataResource

• Classification: LIPID BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMmpstruc


• Deposited: 2020-01-03 Released: 2021-04-21 
• Deposition Author(s): Xia, S., Ruan, J., Wu, H.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Gasdermin D pore structure reveals preferential release of mature interleukin-1.

Xia, S., Zhang, Z., Magupalli, V.G., Pablo, J.L., Dong, Y., Vora, S.M., Wang, L., Fu, T.M., Jacobson, M.P., Greka, A., Lieberman, J., Ruan, J., Wu, H.

(2021) Nature 593: 607-611

• PubMed: 33883744 
• DOI: https://doi.org/10.1038/s41586-021-03478-3
• Primary Citation of Related Structures:  
  6VFE


• PubMed Abstract: 
  

As organelles of the innate immune system, inflammasomes activate caspase-1 and other inflammatory caspases that cleave gasdermin D (GSDMD). Caspase-1 also cleaves inactive precursors of the interleukin (IL)-1 family to generate mature cytokines such as IL-1β and IL-18. Cleaved GSDMD forms transmembrane pores to enable the release of IL-1 and to drive cell lysis through pyroptosis ^1-9 . Here we report cryo-electron microscopy structures of the pore and the prepore of GSDMD. These structures reveal the different conformations of the two states, as well as extensive membrane-binding elements including a hydrophobic anchor and three positively charged patches. The GSDMD pore conduit is predominantly negatively charged. By contrast, IL-1 precursors have an acidic domain that is proteolytically removed by caspase-1 ¹⁰ . When permeabilized by GSDMD pores, unlysed liposomes release positively charged and neutral cargoes faster than negatively charged cargoes of similar sizes, and the pores favour the passage of IL-1β and IL-18 over that of their precursors. Consistent with these findings, living-but not pyroptotic-macrophages preferentially release mature IL-1β upon perforation by GSDMD. Mutation of the acidic residues of GSDMD compromises this preference, hindering intracellular retention of the precursor and secretion of the mature cytokine. The GSDMD pore therefore mediates IL-1 release by electrostatic filtering, which suggests the importance of charge in addition to size in the transport of cargoes across this large channel.

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Organizational Affiliation: 

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C33  (3D View)
Global Stoichiometry: Homo 33-mer - A33 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 886.06 kDa 
• Atom Count: 61,908 
• Modelled Residue Count: 7,887 
• Deposited Residue Count: 7,953 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gasdermin-D, N-terminal	A, AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, EA [auth e], F, FA [auth f], G, GA [auth g], H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	241	Homo sapiens	Mutation(s): 1  Gene Names: GSDMD, DFNA5L, GSDMDC1, FKSG10 Membrane Entity: Yes
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: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-04-21 
Deposition Author(s): Xia, S., Ruan, J., Wu, H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI139914
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)	United States	DP1HD087988
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI124491

Revision History  

• Version 1.0: 2021-04-21
  Type: Initial release
  
• Version 1.1: 2021-05-05
  Changes: Database references
• Version 1.2: 2021-05-12
  Changes: Database references, Structure summary
• Version 2.0: 2021-05-26
  Type: Coordinate replacement
  Reason: Sequence discrepancy
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Structure summary
• Version 2.1: 2021-06-09
  Changes: Database references