4V4L

Structure of the Drosophila apoptosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the Drosophila apoptosome at 6.9 angstrom resolution

Yuan, S.Yu, X.Topf, M.Dorstyn, L.Kumar, S.Ludtke, S.J.Akey, C.W.

(2011) Structure 19: 128-140

  • DOI: 10.1016/j.str.2010.10.009
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Drosophila Apaf-1 related killer forms an apoptosome in the intrinsic cell death pathway. In this study we show that Dark forms a single ring when initiator procaspases are bound. This Dark-Dronc complex cleaves DrICE efficiently; hence, a single ...

    The Drosophila Apaf-1 related killer forms an apoptosome in the intrinsic cell death pathway. In this study we show that Dark forms a single ring when initiator procaspases are bound. This Dark-Dronc complex cleaves DrICE efficiently; hence, a single ring represents the Drosophila apoptosome. We then determined the 3D structure of a double ring at ∼6.9 Å resolution and created a model of the apoptosome. Subunit interactions in the Dark complex are similar to those in Apaf-1 and CED-4 apoptosomes, but there are significant differences. In particular, Dark has "lost" a loop in the nucleotide-binding pocket, which opens a path for possible dATP exchange in the apoptosome. In addition, caspase recruitment domains (CARDs) form a crown on the central hub of the Dark apoptosome. This CARD geometry suggests that conformational changes will be required to form active Dark-Dronc complexes. When taken together, these data provide insights into apoptosome structure, function, and evolution.


    Organizational Affiliation

    Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Apaf-1 related killer DARK
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
1221Drosophila melanogasterMutation(s): 0 
Gene Names: Dark (anon-53Fa, Apaf, APAF-1, Apaf-1, apaf-1, Apaf-I, APAF1, Apaf1, apaf1, arc, ARK, Ark, ark, Ark-RB, D-Apaf-1, dapaf, Dapaf-1, dAPAF-1, dApaf-1, dapaf-1, dapaf-1L, dapaf-1S, dApaf1, DARK, dArk, dark, Dmel\CG6829, HAC-1, Hac-1, hac-1, HAC1, Hac1, hac1, l(2)SH0173, T1)
Find proteins for Q7KLI1 (Drosophila melanogaster)
Go to UniProtKB:  Q7KLI1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DTP
Query on DTP

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Other
  • Version 1.2: 2018-07-18
    Type: Data collection, Database references