5JQE | pdb_00005jqe

Crystal structure of caspase8 tDED

• PDB DOI: https://doi.org/10.2210/pdb5JQE/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-05-04 Released: 2016-10-26 
• Deposition Author(s): Fu, T., Li, Y., Lu, A., Wu, H.
• Funding Organization(s): National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.16 Å
• R-Value Free: 
  0.274 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: other

Literature

Cryo-EM Structure of Caspase-8 Tandem DED Filament Reveals Assembly and Regulation Mechanisms of the Death-Inducing Signaling Complex.

Fu, T.M., Li, Y., Lu, A., Li, Z., Vajjhala, P.R., Cruz, A.C., Srivastava, D.B., DiMaio, F., Penczek, P.A., Siegel, R.M., Stacey, K.J., Egelman, E.H., Wu, H.

(2016) Mol Cell 64: 236-250

• PubMed: 27746017 
• DOI: https://doi.org/10.1016/j.molcel.2016.09.009
• Primary Citation Related Structures: 
  5JQE, 5L08


• PubMed Abstract: 
  

  Caspase-8 activation can be triggered by death receptor-mediated formation of the death-inducing signaling complex (DISC) and by the inflammasome adaptor ASC. Caspase-8 assembles with FADD at the DISC and with ASC at the inflammasome through its tandem death effector domain (tDED), which is regulated by the tDED-containing cellular inhibitor cFLIP and the viral inhibitor MC159. Here we present the caspase-8 tDED filament structure determined by cryoelectron microscopy. Extensive assembly interfaces not predicted by the previously proposed linear DED chain model were uncovered, and were further confirmed by structure-based mutagenesis in filament formation in vitro and Fas-induced apoptosis and ASC-mediated caspase-8 recruitment in cells. Structurally, the two DEDs in caspase-8 use quasi-equivalent contacts to enable assembly. Using the tDED filament structure as a template, structural analyses reveal the interaction surfaces between FADD and caspase-8 and the distinct mechanisms of regulation by cFLIP and MC159 through comingling and capping, respectively.

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Organizational Affiliation: 
• Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia.
Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA.
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
Department of Biochemistry and Molecular Biology, University of Texas-Houston Medical School, Houston, TX 77030, USA.
School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia; Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia.
Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 63.71 kDa 
• Atom Count: 4,316 
• Modeled Residue Count: 544 
• Deposited Residue Count: 565 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sugar ABC transporter substrate-binding protein,Caspase-8 chimera	A	565	Escherichia coli	Mutation(s): 0  Gene Names: malE, AC066_14980, CASP8, MCH5 EC: 3.4.22.61
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for Q14790 (Homo sapiens) Explore Q14790  Go to UniProtKB:  Q14790
PHAROS:  Q14790 GTEx:  ENSG00000064012
UniProt Groups	Q14790P0AEX9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.16 Å
• R-Value Free:  0.274 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.923	α = 90
b = 130.923	β = 90
c = 67.956	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-10-26 
Deposition Author(s): Fu, T., Li, Y., Lu, A., Wu, H.

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Funding Organization	Location	Grant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)	United States	DP1-HD087988
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R37-AI050872
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01-AI045937
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)	United States	R01-EB001567

Revision History  

• Version 1.0: 2016-10-26
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2018-02-21
  Changes: Database references
• Version 1.3: 2022-03-23
  Changes: Author supporting evidence, Database references
• Version 1.4: 2024-04-03
  Changes: Data collection, Refinement description