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- EMDB-38995: Structure of the Dark/Dronc complex -

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Basic information

Entry
Database: EMDB / ID: EMD-38995
TitleStructure of the Dark/Dronc complex
Map data
Sample
  • Complex: Structure of the Dark/Dronc complex
    • Complex: Dronc-CARD
      • Protein or peptide: Caspase Dronc
    • Complex: Dark
      • Protein or peptide: Apaf-1 related killer DARK
KeywordsDark / Dronc / apoptosis / cryo-EM
Function / homology
Function and homology information


hemocyte development / nurse cell apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / negative regulation of humoral immune response / positive regulation of glial cell apoptotic process / head involution / positive regulation of compound eye retinal cell programmed cell death / Formation of apoptosome / embryonic development via the syncytial blastoderm / salivary gland histolysis ...hemocyte development / nurse cell apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / negative regulation of humoral immune response / positive regulation of glial cell apoptotic process / head involution / positive regulation of compound eye retinal cell programmed cell death / Formation of apoptosome / embryonic development via the syncytial blastoderm / salivary gland histolysis / melanization defense response / caspase-9 / sarcosine catabolic process / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity / central nervous system formation / positive regulation of apoptotic process involved in development / metamorphosis / compound eye development / chaeta development / sperm individualization / apoptosome / autophagic cell death / programmed cell death involved in cell development / Neutrophil degranulation / programmed necrotic cell death / S-adenosylmethionine cycle / CARD domain binding / : / programmed cell death / triglyceride homeostasis / : / zymogen activation / dendrite morphogenesis / neuron remodeling / response to starvation / cysteine-type endopeptidase activator activity involved in apoptotic process / protein autoprocessing / ectopic germ cell programmed cell death / central nervous system development / determination of adult lifespan / response to gamma radiation / ADP binding / neuron cellular homeostasis / endopeptidase activity / positive regulation of apoptotic process / cysteine-type endopeptidase activity / negative regulation of cell population proliferation / apoptotic process / protein homodimerization activity / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
: / : / Dark, CARD domain / Dark, winged-helix domain / APAF-1 helical domain / APAF-1 helical domain / NB-ARC / NB-ARC domain / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site ...: / : / Dark, CARD domain / Dark, winged-helix domain / APAF-1 helical domain / APAF-1 helical domain / NB-ARC / NB-ARC domain / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Death-like domain superfamily / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Apoptosome protein Dark / Caspase Dronc
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.0 Å
AuthorsTian L / Li Y / Shi Y
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: 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
DepositionFeb 3, 2024-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38995.png

Downloads & links

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Map

FileDownload / File: emd_38995.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 440 pix.
= 426.8 Å		0.97 Å/pix.
x 440 pix.
= 426.8 Å		0.97 Å/pix.
x 440 pix.
= 426.8 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.23311351 - 0.5296398
Average (Standard dev.)0.0009607445 (±0.037931908)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 426.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38995_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38995_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of the Dark/Dronc complex

EntireName: Structure of the Dark/Dronc complex
Components
  • Complex: Structure of the Dark/Dronc complex
    • Complex: Dronc-CARD
      • Protein or peptide: Caspase Dronc
    • Complex: Dark
      • Protein or peptide: Apaf-1 related killer DARK

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Supramolecule #1: Structure of the Dark/Dronc complex

SupramoleculeName: Structure of the Dark/Dronc complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Supramolecule #2: Dronc-CARD

SupramoleculeName: Dronc-CARD / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2

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Supramolecule #3: Dark

SupramoleculeName: Dark / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1

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Macromolecule #1: Apaf-1 related killer DARK

MacromoleculeName: Apaf-1 related killer DARK / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 142.710344 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: YQYKDILSVF EDAFVDNFDC KDVQDMPKSI LSKEEIDHII MSKDAVSGTL RLFWTLLSKQ EEMVQKFVEE VLRINYKFLM SPIKTEQRQ PSMMTRMYIE QRDRLYNDNQ VFAKYNVSRL QPYLKLRQAL LELRPAKNVL IDGVLGSGKT WVALDVCLSY K VQCKMDFK ...String:
YQYKDILSVF EDAFVDNFDC KDVQDMPKSI LSKEEIDHII MSKDAVSGTL RLFWTLLSKQ EEMVQKFVEE VLRINYKFLM SPIKTEQRQ PSMMTRMYIE QRDRLYNDNQ VFAKYNVSRL QPYLKLRQAL LELRPAKNVL IDGVLGSGKT WVALDVCLSY K VQCKMDFK IFWLNLKNCN SPETVLEMLQ KLLYQIDPNW TSRSDHSSNI KLRIHSIQAE LRRLLKSKPY ENCLLVLLNV QN AKAWNAF NLSCKILLTT RFKQVTDFLS AATTTHISLD HHSMTLTPDE VKSLLLKYLD CRPQDLPREV LTTNPRRLSI IAE SIRDGL ATWDNWKHVN CDKLTTIIES SLNVLEPAEY RKMFDRLSVF PPSAHIPTIL LSLIWFDVIK SDVMVVVNKL HKYS LVEKQ PKESTISIPS IYLELKVKLE NEYALHRSIV DHYNIPKTFD SDDLIPPYLD QYFYSHIGHH LKNIEHPERM TLFRM VFLD FRFLEQKIRH DSTAWNASGS ILNTLQQLKF YKPYICDNDP KYERLVNAIL DFLPKIEENL ICSKYTDLLR IALMAE DEA IFEEAHKQVQ RFDDRVWFTN HGRFHQHRQI INLGDNEGRH AVYLHNDFCL IALASGQILL TDVSLEGEDT YLLRDES DS SDILRMAVFN QQKHLITLHC NGSVKLWSLW PDCPGRRHSG GSKQQLVNSV VKRFIGSYAN LKIVAFYLNE DAGLPEAN I QLHVAFINGD VSILNWDEQD QEFKLSHVPV LKTMQSGIRC FVQVLKRYYV VCTSNCTLTV WDLTNGSSNT LELHVFNVE NDTPLALDVF DERSKTATVL LIFKYSVWRL NFLPGLSVSL QSEAVQLPEG SFITCGKRST DGRYLLLGTS EGLIVYDLKI SDPVLRSNV SEHIECVDIY ELFDPVYKYI VLCGAKGKQV VHVHTLRSVS GSNSHQNREI AWVHSADEIS VMTKACLEPN V YLRSLMDM TRERTQLLAV DSKERIHLIK PAISRISEWS TITPTHAASN CKINAISAFN DEQIFVGYVD GVIIDVIHDT AL PQQFIEE PIDYLKQVSP NILVASAHSA QKTVIFQLEK IDPLQPNDQW PLMMDVSTKY ASLQEGQYII LFSDHGVCHL DIA NPSAFV KPKDSEEYIV GFDLKNSLLF LAYENNIIDV FRLIFSCNQL RYEQICEEEI AQKAKISYLV ATDDGTMLAM GFEN GTLEL FAVENRKVQL IYSIEEVHEH CIRQLLFSPC KL

UniProtKB: Apoptosome protein Dark

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Macromolecule #2: Caspase Dronc

MacromoleculeName: Caspase Dronc / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 12.039956 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPKRHREHIR KNLNILVEWT NYERLAMECV QQGILTVQML RNTQDLNGKP FNMDEKDVRV EQHRRLLLKI TQRGPTAYNL LINALRNIN CLDAAVLLES VDE

UniProtKB: Caspase Dronc

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3j9k

Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2710
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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