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Open data
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Basic information
Entry | Database: PDB / ID: 3j9k | ||||||
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Title | Structure of Dark apoptosome in complex with Dronc CARD domain | ||||||
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Function / homology | ![]() hemocyte development / TP53 Regulates Transcription of Caspase Activators and Caspases / nurse cell apoptotic process / negative regulation of humoral immune response / positive regulation of glial cell apoptotic process / Formation of apoptosome / : / head involution / embryonic development via the syncytial blastoderm / salivary gland histolysis ...hemocyte development / TP53 Regulates Transcription of Caspase Activators and Caspases / nurse cell apoptotic process / negative regulation of humoral immune response / positive regulation of glial cell apoptotic process / Formation of apoptosome / : / head involution / embryonic development via the syncytial blastoderm / salivary gland histolysis / positive regulation of compound eye retinal cell programmed cell death / melanization defense response / sarcosine catabolic process / Regulation of the apoptosome activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
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Method | ![]() ![]() ![]() | ||||||
![]() | Pang, Y. / Bai, X. / Yan, C. / Hao, Q. / Chen, Z. / Wang, J. / Scheres, S.H.W. / Shi, Y. | ||||||
![]() | ![]() Title: Structure of the apoptosome: mechanistic insights into activation of an initiator caspase from Drosophila. Authors: Yuxuan Pang / Xiao-chen Bai / Chuangye Yan / Qi Hao / Zheqin Chen / Jia-Wei Wang / Sjors H W Scheres / Yigong Shi / ![]() ![]() Abstract: Apoptosis is executed by a cascade of caspase activation. The autocatalytic activation of an initiator caspase, exemplified by caspase-9 in mammals or its ortholog, Dronc, in fruit flies, is ...Apoptosis is executed by a cascade of caspase activation. The autocatalytic activation of an initiator caspase, exemplified by caspase-9 in mammals or its ortholog, Dronc, in fruit flies, is facilitated by a multimeric adaptor complex known as the apoptosome. The underlying mechanism by which caspase-9 or Dronc is activated by the apoptosome remains unknown. Here we report the electron cryomicroscopic (cryo-EM) structure of the intact apoptosome from Drosophila melanogaster at 4.0 Å resolution. Analysis of the Drosophila apoptosome, which comprises 16 molecules of the Dark protein (Apaf-1 ortholog), reveals molecular determinants that support the assembly of the 2.5-MDa complex. In the absence of dATP or ATP, Dronc zymogen potently induces formation of the Dark apoptosome, within which Dronc is efficiently activated. At 4.1 Å resolution, the cryo-EM structure of the Dark apoptosome bound to the caspase recruitment domain (CARD) of Dronc (Dronc-CARD) reveals two stacked rings of Dronc-CARD that are sandwiched between two octameric rings of the Dark protein. The specific interactions between Dronc-CARD and both the CARD and the WD40 repeats of a nearby Dark protomer are indispensable for Dronc activation. These findings reveal important mechanistic insights into the activation of initiator caspase by the apoptosome. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 3.1 MB | Display | ![]() |
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PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2870MC ![]() 2871C ![]() 3j9lC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
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Components
#1: Protein | Mass: 112749.156 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #2: Protein | Mass: 51207.145 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() References: UniProt: Q9XYF4, ![]() #3: Chemical | ChemComp-ADP / ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
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Molecular weight | Value: 3 MDa / Experimental value: NO | ||||||||||||||||
Buffer solution | Name: 25 mM Tris, pH 8.0, 150 mM NaCl, 5 mM DTT / pH: 8 / Details: 25 mM Tris, pH 8.0, 150 mM NaCl, 5 mM DTT | ||||||||||||||||
Specimen | Conc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | ||||||||||||||||
Specimen support | Details: glow-discharged holey carbon grids (Quantifoil CuR2/2) with home-made continuous carbon film | ||||||||||||||||
Vitrification![]() | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temp: 85 K / Humidity: 100 % Details: Blot for 2 seconds before plunging into liquid ethane (FEI VITROBOT MARK II). Method: Blot for 2 seconds before plunging |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 / Date: Jan 8, 2014 |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() ![]() |
Specimen holder | Specimen holder model: GATAN LIQUID NITROGEN / Temperature: 85 K / Temperature (max): 90 K / Temperature (min): 80 K |
Image recording | Electron dose: 28 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
Image scans | Num. digital images: 1234 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
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Processing
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CTF correction![]() | Details: Each particle | ||||||||||||
Symmetry | Point symmetry![]() ![]() | ||||||||||||
3D reconstruction![]() | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11359 / Nominal pixel size: 1.34 Å / Actual pixel size: 1.34 Å Details: To correct for beam-induced movements, the 16 video frames for each micrograph were first aligned using whole-image motion correction. Then particle-based beam-induced movement correction ...Details: To correct for beam-induced movements, the 16 video frames for each micrograph were first aligned using whole-image motion correction. Then particle-based beam-induced movement correction was performed using statistical movie processing in RELION. Symmetry type: POINT | ||||||||||||
Refinement step | Cycle: LAST
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