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- EMDB-38994: Structure of the auto-inhibited Dark monomer -

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Basic information

Entry
Database: EMDB / ID: EMD-38994
TitleStructure of the auto-inhibited Dark monomer
Map data
Sample
  • Complex: Structure of the auto-inhibited Dark monomer
    • Protein or peptide: Apaf-1 related killer DARK
KeywordsDark / apoptosis / 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 / melanization defense response / sarcosine catabolic process / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity / compound eye retinal cell programmed cell death / central nervous system formation ...negative regulation of humoral immune response / positive regulation of glial cell apoptotic process / Formation of apoptosome / salivary gland histolysis / melanization defense response / sarcosine catabolic process / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity / compound eye retinal cell programmed cell death / central nervous system formation / positive regulation of apoptotic process involved in development / chaeta development / sperm individualization / apoptosome / autophagic cell death / Neutrophil degranulation / S-adenosylmethionine cycle / CARD domain binding / programmed cell death / triglyceride homeostasis / response to starvation / dendrite morphogenesis / response to gamma radiation / neuron cellular homeostasis / ADP binding / apoptotic process / structural molecule activity / ATP binding / identical protein binding
Similarity search - Function
: / : / Dark, CARD domain / Dark, winged-helix domain / APAF-1 helical domain / APAF-1 helical domain / NB-ARC / NB-ARC domain / WD40 repeats / WD40 repeat ...: / : / Dark, CARD domain / Dark, winged-helix domain / APAF-1 helical domain / APAF-1 helical domain / NB-ARC / NB-ARC domain / WD40 repeats / WD40 repeat / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Apoptosome protein Dark
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 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) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38994.png

Downloads & links

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Map

FileDownload / File: emd_38994.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 256 pix.
= 248.32 Å		0.97 Å/pix.
x 256 pix.
= 248.32 Å		0.97 Å/pix.
x 256 pix.
= 248.32 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.21
Minimum - Maximum-0.6202567 - 1.0517192
Average (Standard dev.)0.0003593607 (±0.031358846)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 248.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38994_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_38994_half_map_2.map
Projections & Slices
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Sample components

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Entire : Structure of the auto-inhibited Dark monomer

EntireName: Structure of the auto-inhibited Dark monomer
Components
  • Complex: Structure of the auto-inhibited Dark monomer
    • Protein or peptide: Apaf-1 related killer DARK

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Supramolecule #1: Structure of the auto-inhibited Dark monomer

SupramoleculeName: Structure of the auto-inhibited Dark monomer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 166.603641 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDFETGEHQY QYKDILSVFE DAFVDNFDCK DVQDMPKSIL SKEEIDHIIM SKDAVSGTLR LFWTLLSKQE EMVQKFVEEV LRINYKFLM SPIKTEQRQP SMMTRMYIEQ RDRLYNDNQV FAKYNVSRLQ PYLKLRQALL ELRPAKNVLI DGVLGSGKTW V ALDVCLSY ...String:
MDFETGEHQY QYKDILSVFE DAFVDNFDCK DVQDMPKSIL SKEEIDHIIM SKDAVSGTLR LFWTLLSKQE EMVQKFVEEV LRINYKFLM SPIKTEQRQP SMMTRMYIEQ RDRLYNDNQV FAKYNVSRLQ PYLKLRQALL ELRPAKNVLI DGVLGSGKTW V ALDVCLSY KVQCKMDFKI FWLNLKNCNS PETVLEMLQK LLYQIDPNWT SRSDHSSNIK LRIHSIQAEL RRLLKSKPYE NC LLVLLNV QNAKAWNAFN LSCKILLTTR FKQVTDFLSA ATTTHISLDH HSMTLTPDEV KSLLLKYLDC RPQDLPREVL TTN PRRLSI IAESIRAGLA TWDNWKHVNC DKLTTIIESS LNVLEPAEYR KMFDRLSVFP PSAHIPTILL SLIWFDVIKS DVMV VVNKL HKYSLVEKQP KESTISIPSI YLELKVKLEN EYALHRSIVD HYNIPKTFDS DDLIPPYLDQ YFYSHIGHHL KNIEH PERM TLFRMVFLDF RFLEQKIRHD STAWNASGSI LNTLQQLKFY KPYICDNDPK YERLVNAILD FLPKIEENLI CSKYTD LLR IALMAEDEAI FEEAHKQVQR FDDRVWFTNH GRFHQHRQII NLGDNEGRHA VYLHNDFCLI ALASGQILLT DVSLEGE DT YLLRDESDSS DILRMAVFNQ QKHLITLHCN GSVKLWSLWP DCPGRRHSGG SKQQLVNSVV KRFIGSYANL KIVAFYLN E DAGLPEANIQ LHVAFINGDV SILNWDEQDQ EFKLSHVPVL KTMQSGIRCF VQVLKRYYVV CTSNCTLTVW DLTNGSSNT LELHVFNVEN DTPLALDVFD ERSKTATVLL IFKYSVWRLN FLPGLSVSLQ SEAVQLPEGS FITCGKRSTD GRYLLLGTSE GLIVYDLKI SDPVLRSNVS EHIECVDIYE LFDPVYKYIV LCGAKGKQVV HVHTLRSVSG SNSHQNREIA WVHSADEISV M TKACLEPN VYLRSLMDMT RERTQLLAVD SKERIHLIKP AISRISEWST ITPTHAASNC KINAISAFND EQIFVGYVDG VI IDVIHDT ALPQQFIEEP IDYLKQVSPN ILVASAHSAQ KTVIFQLEKI DPLQPNDQWP LMMDVSTKYA SLQEGQYIIL FSD HGVCHL DIANPSAFVK PKDSEEYIVG FDLKNSLLFL AYENNIIDVF RLIFSCNQLR YEQICEEEIA QKAKISYLVA TDDG TMLAM GFENGTLELF AVENRKVQLI YSIEEVHEHC IRQLLFSPCK LLLISCAEQL CFWNVTHMRN NQLEREQKRR RSRRH KQHS VTQEDAVDAA PIAADIDVDV TFVADEFHPV NRGTAELWRN KRGNAIRPEL LACVKFVGNE ARQFFTDAHF SHFYAI DDE GVYYHLQLLE LSRLQPPPDP VTLDIANQYE DLKNLRILDS PLMQDSDSEG ADVVGNLVLE KNGGVARATP ILEEASS HH HHHH

UniProtKB: Apoptosome protein Dark

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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:

3j9l

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 105018
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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