[English] 日本語
Yorodumi
- EMDB-38995: Structure of the Dark/Dronc complex -

+
Open data


ID or keywords:

Loading...

-
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 / 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 ...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 / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity / central nervous system formation / 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 / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / 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 / regulation of autophagy / central nervous system development / determination of adult lifespan / response to gamma radiation / ADP binding / neuron cellular homeostasis / endopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / positive regulation of apoptotic process / negative regulation of cell population proliferation / cysteine-type endopeptidase activity / apoptotic process / protein homodimerization activity / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
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 ...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
Apaf-1 related killer 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

-
Structure visualization

Supplemental images

emd_38995.png

Downloads & links

-
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
Brightness
Contrast
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

Slices (1/3)

Slices (1/2)

Slices (2/3)

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 °

-
Supplemental data

-
Half map: #2

Fileemd_38995_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_38995_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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)

-
Supramolecule #2: Dronc-CARD

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

-
Supramolecule #3: Dark

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

-
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: Apaf-1 related killer DARK

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
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

+
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more