8Y6Q | pdb_00008y6q

Structure of the Dark/Dronc complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8Y6Q

This is version 1.0 of the entry. See complete history

Literature

Dark and Dronc activation in Drosophila melanogaster.

Tian, L.Li, Y.Shi, Y.

(2024) Proc Natl Acad Sci U S A 121: e2312784121-e2312784121

  • DOI: https://doi.org/10.1073/pnas.2312784121
  • Primary Citation Related Structures: 
    8Y6P, 8Y6Q

  • PubMed Abstract: 

    The onset of apoptosis is characterized by a cascade of caspase activation, where initiator caspases are activated by a multimeric adaptor complex known as the apoptosome. In Drosophila melanogaster , the initiator caspase Dronc undergoes autocatalytic activation in the presence of the Dark apoptosome. Despite rigorous investigations, the activation mechanism for Dronc remains elusive. Here, we report the cryo-EM structures of an auto-inhibited Dark monomer and a single-layered, multimeric Dark/Dronc complex. Our biochemical analysis suggests that the auto-inhibited Dark oligomerizes upon binding to Dronc, which is sufficient for the activation of both Dark and Dronc. In contrast, the previously observed double-ring Dark apoptosome may represent a non-functional or "off-pathway" conformation. These findings expand our understanding on the molecular mechanism of apoptosis in Drosophila .


  • Organizational Affiliation
    • Beijing Frontier Research Center for Biological Structures, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.

Macromolecule Content 

  • Total Structure Weight: 1,238 kDa 
  • Atom Count: 75,726 
  • Modeled Residue Count: 9,362 
  • Deposited Residue Count: 10,712 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Apaf-1 related killer DARK1,237Drosophila melanogasterMutation(s): 0 
Gene Names: 
UniProt
Find proteins for Q7KLI1 (Drosophila melanogaster)
Explore Q7KLI1 
Go to UniProtKB:  Q7KLI1
Entity Groups
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UniProt GroupQ7KLI1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Caspase Dronc102Drosophila melanogasterMutation(s): 0 
Gene Names: DroncNcCG8091
EC: 3.4.22 (PDB Primary Data), 3.4.22.62 (UniProt)
UniProt
Find proteins for Q9XYF4 (Drosophila melanogaster)
Explore Q9XYF4 
Go to UniProtKB:  Q9XYF4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XYF4
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-07
    Type: Initial release