+Open data
-Basic information
Entry | Database: PDB / ID: 8y6p | ||||||
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Title | Structure of the auto-inhibited Dark monomer | ||||||
Components | Apaf-1 related killer DARK | ||||||
Keywords | APOPTOSIS / Dark / cryo-EM | ||||||
Function / homology | Function and homology information negative regulation of humoral immune response / positive regulation of glial cell apoptotic process / Formation of apoptosome / salivary gland histolysis / positive regulation of compound eye retinal cell programmed cell death / melanization defense response / sarcosine catabolic process / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity / central nervous system formation ...negative regulation of humoral immune response / positive regulation of glial cell apoptotic process / Formation of apoptosome / salivary gland histolysis / positive regulation of compound eye retinal cell programmed cell death / melanization defense response / sarcosine catabolic process / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity / central nervous system formation / chaeta development / sperm individualization / apoptosome / autophagic cell death / Neutrophil degranulation / S-adenosylmethionine cycle / CARD domain binding / programmed cell death / triglyceride homeostasis / dendrite morphogenesis / response to starvation / cysteine-type endopeptidase activator activity involved in apoptotic process / response to gamma radiation / ADP binding / neuron cellular homeostasis / positive regulation of apoptotic process / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
Authors | Tian, L. / Li, Y. / Shi, Y. | ||||||
Funding support | 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2024 Title: Dark and Dronc activation in . Authors: Lu Tian / Yini Li / Yigong Shi / 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 , the initiator caspase ...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 , 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 . | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8y6p.cif.gz | 235.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8y6p.ent.gz | 184.6 KB | Display | PDB format |
PDBx/mmJSON format | 8y6p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8y6p_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8y6p_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8y6p_validation.xml.gz | 50.7 KB | Display | |
Data in CIF | 8y6p_validation.cif.gz | 74.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/8y6p ftp://data.pdbj.org/pub/pdb/validation_reports/y6/8y6p | HTTPS FTP |
-Related structure data
Related structure data | 38994MC 8y6qC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 166603.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) Gene: Dark, anon-53Fa, Apaf, APAF-1, Apaf-1, apaf-1, APAF1, Apaf1, apaf1, arc, ARK, Ark, ark, Ark-RB, D-Apaf-1, dapaf, Dapaf-1, dAPAF-1, dApaf-1, dapaf-1, dApaf-1/DARK/HAC-1, Dapaf-1/HAC-1, dapaf-1L, ...Gene: Dark, anon-53Fa, Apaf, APAF-1, Apaf-1, apaf-1, APAF1, Apaf1, apaf1, arc, ARK, Ark, ark, Ark-RB, D-Apaf-1, dapaf, Dapaf-1, dAPAF-1, dApaf-1, dapaf-1, dApaf-1/DARK/HAC-1, Dapaf-1/HAC-1, dapaf-1L, dapaf-1S, dApaf1, DARK, dArk, dark, Dark/Apaf-I, dark/dapaf-1/hac-1, Dark/Dapaf-1/HAC1, Dark/Hac-1/dApaf-1, dark/hac-1/dapaf-1, Dark/Hac-1/dApaf1, Dmel\CG6829, Hac-1, hac-1, Hac-1/Dark, Hac1, hac1, l(2)SH0173, T1, CG6829, Dmel_CG6829 Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q7KLI1 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Structure of the auto-inhibited Dark monomer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 105018 / Symmetry type: POINT |