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- EMDB-36459: cryo-EM structure of the CED-4/CED-3 holoenzyme -

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Basic information

Entry
Database: EMDB / ID: EMD-36459
Titlecryo-EM structure of the CED-4/CED-3 holoenzyme
Map data
Sample
  • Complex: ternary complex of CED-4 with CED-3 CARD and CED-3 catalytic domain
    • Protein or peptide: Cell death protein 4
    • Protein or peptide: Cell death protein 3
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsCED-4 / CED-3 / holoenzyme / APOPTOSIS
Function / homology
Function and homology information


negative regulation of cellular response to manganese ion / positive regulation of cellular response to gamma radiation / Apoptotic cleavage of cellular proteins / Apoptosis induced DNA fragmentation / Signaling by Hippo / Caspase-mediated cleavage of cytoskeletal proteins / Caspase activation via Dependence Receptors in the absence of ligand / Regulation of TNFR1 signaling / Apoptotic cleavage of cell adhesion proteins / positive regulation of egg-laying behavior ...negative regulation of cellular response to manganese ion / positive regulation of cellular response to gamma radiation / Apoptotic cleavage of cellular proteins / Apoptosis induced DNA fragmentation / Signaling by Hippo / Caspase-mediated cleavage of cytoskeletal proteins / Caspase activation via Dependence Receptors in the absence of ligand / Regulation of TNFR1 signaling / Apoptotic cleavage of cell adhesion proteins / positive regulation of egg-laying behavior / BH1 domain binding / regulation of vulval development / positive regulation of apoptotic process involved in development / regulation of development, heterochronic / positive regulation of synapse pruning / caspase complex / peptidase activator activity involved in apoptotic process / caspase-7 / regulation of cell fate specification / positive regulation of protein processing / caspase binding / embryonic morphogenesis / programmed cell death / apoptotic process involved in development / negative regulation of execution phase of apoptosis / actin filament depolymerization / activation of cysteine-type endopeptidase activity / cysteine-type endopeptidase activity involved in execution phase of apoptosis / embryo development ending in birth or egg hatching / execution phase of apoptosis / regulation of locomotion / regulation of cell size / muscle cell cellular homeostasis / regulation of synapse organization / BH3 domain binding / cysteine-type endopeptidase activator activity involved in apoptotic process / protein autoprocessing / endopeptidase activator activity / regulation of cell adhesion / ADP binding / protein catabolic process / regulation of protein stability / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of neuron apoptotic process / presynapse / perikaryon / nuclear membrane / endopeptidase activity / defense response to Gram-negative bacterium / positive regulation of apoptotic process / cysteine-type endopeptidase activity / neuronal cell body / apoptotic process / negative regulation of apoptotic process / perinuclear region of cytoplasm / magnesium ion binding / protein-containing complex / mitochondrion / proteolysis / ATP binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Apoptosis regulator, Ced-4 / NB-ARC / NB-ARC domain / Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 ...Apoptosis regulator, Ced-4 / NB-ARC / NB-ARC domain / Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Peptidase family C14A, His active site / Caspase family histidine active site. / 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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Cell death protein 4 / Cell death protein 3
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsLi Y / Tian L / Zhang Y / Shi Y
Funding support China, 1 items
OrganizationGrant numberCountry
Other private China
Citation
Journal: Life Sci Alliance / Year: 2023
Title: Structural insights into CED-3 activation.
Authors: Yini Li / Lu Tian / Ying Zhang / Yigong Shi /
Abstract: In , onset of programmed cell death is marked with the activation of CED-3, a process that requires assembly of the CED-4 apoptosome. Activated CED-3 forms a holoenzyme with the CED-4 apoptosome to ...In , onset of programmed cell death is marked with the activation of CED-3, a process that requires assembly of the CED-4 apoptosome. Activated CED-3 forms a holoenzyme with the CED-4 apoptosome to cleave a wide range of substrates, leading to irreversible cell death. Despite decades of investigations, the underlying mechanism of CED-4-facilitated CED-3 activation remains elusive. Here, we report cryo-EM structures of the CED-4 apoptosome and three distinct CED-4/CED-3 complexes that mimic different activation stages for CED-3. In addition to the previously reported octamer in crystal structures, CED-4, alone or in complex with CED-3, exists in multiple oligomeric states. Supported by biochemical analyses, we show that the conserved CARD-CARD interaction promotes CED-3 activation, and initiation of programmed cell death is regulated by the dynamic organization of the CED-4 apoptosome.
#1: Journal: Life Sci Alliance / Year: 2023
Title: Structural insights into CED-3 activation
Authors: Li Y / Tian L / Zhang Y / Shi Y
History
DepositionJun 7, 2023-
Header (metadata) releaseJun 28, 2023-
Map releaseJun 28, 2023-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36459.png

Downloads & links

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Map

FileDownload / File: emd_36459.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.32 Å
Density
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.017552694 - 0.073837265
Average (Standard dev.)0.00011148205 (±0.002446653)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 337.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_36459_additional_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_36459_half_map_1.map
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36459_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : ternary complex of CED-4 with CED-3 CARD and CED-3 catalytic domain

EntireName: ternary complex of CED-4 with CED-3 CARD and CED-3 catalytic domain
Components
  • Complex: ternary complex of CED-4 with CED-3 CARD and CED-3 catalytic domain
    • Protein or peptide: Cell death protein 4
    • Protein or peptide: Cell death protein 3
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: ternary complex of CED-4 with CED-3 CARD and CED-3 catalytic domain

SupramoleculeName: ternary complex of CED-4 with CED-3 CARD and CED-3 catalytic domain
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

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Macromolecule #1: Cell death protein 4

MacromoleculeName: Cell death protein 4 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 62.953266 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLCEIECRAL STAHTRLIHD FEPRDALTYL EGKNIFTEDH SELISKMSTR LERIANFLRI YRRQASELGP LIDFFNYNNQ SHLADFLED YIDFAINEPD LLRPVVIAPQ FSRQMLDRKL LLGNVPKQMT CYIREYHVDR VIKKLDEMCD LDSFFLFLHG R AGSGKSVI ...String:
MLCEIECRAL STAHTRLIHD FEPRDALTYL EGKNIFTEDH SELISKMSTR LERIANFLRI YRRQASELGP LIDFFNYNNQ SHLADFLED YIDFAINEPD LLRPVVIAPQ FSRQMLDRKL LLGNVPKQMT CYIREYHVDR VIKKLDEMCD LDSFFLFLHG R AGSGKSVI ASQALSKSDQ LIGINYDSIV WLKDSGTAPK STFDLFTDIL LMLKSEDDLL NFPSVEHVTS VVLKRMICNA LI DRPNTLF VFDDVVQEET IRWAQELRLR CLVTTRDVEI SNAASQTCEF IEVTSLEIDE CYDFLEAYGM PMPVGEKEED VLN KTIELS SGNPATLMMF FKSCEPKTFE KMAQLNNKLE SRGLVGVECI TPYSYKSLAM ALQRCVEVLS DEDRSALAFA VVMP PGVDI PVKLWSCVIP VDICSNEEEQ LDDEVADRLK RLSKRGALLS GKRMPVLTFK IDHIIHMFLK HVVDAQTIAN GISIL EQRL LEIGNNNVSV PERHIPSHFQ KFRRSSASEM YPKTTEETVI RPEDFPKFMQ LHQKFYDSLK NFACC

UniProtKB: Cell death protein 4

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Macromolecule #2: Cell death protein 3

MacromoleculeName: Cell death protein 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: caspase-7
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 56.693902 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MMRQDRRSLL ERNIMMFSSH LKVDEILEVL IAKQVLNSDN GDMINSCGTV REKRREIVKA VQRRGDVAFD AFYDALRSTG HEGLAEVLE PLARSVDSNA VEFECPMSPA SHRRSRALSP AGYTSPTRVH RDSVSSVSSF TSYQDIYSRA RSRSRSRALH S SDRHNYSS ...String:
MMRQDRRSLL ERNIMMFSSH LKVDEILEVL IAKQVLNSDN GDMINSCGTV REKRREIVKA VQRRGDVAFD AFYDALRSTG HEGLAEVLE PLARSVDSNA VEFECPMSPA SHRRSRALSP AGYTSPTRVH RDSVSSVSSF TSYQDIYSRA RSRSRSRALH S SDRHNYSS PPVNAFPSQP SSANSSFTGC SSLGYSSSRN RSFSKASGPT QYIFHEEDMN FVDAPTISRV FDEKTMYRNF SS PRGMCLI INNEHFEQMP TRNGTKADKD NLTNLFRCMG YTVICKDNLT GRGMLLTIRD FAKHESHGDS AILVILSHGE ENV IIGVDD IPISTHEIYD LLNAANAPRL ANKPKIVFVQ ACRGERRDNG FPVLDSVDGV PAFLRRGWDN RDGPLFNFLG CVRP QVQQV WRKKPSQADI LIAYATTAQY VSWRNSARGS WFIQAVCEVF STHAKDMDVV ELLTEVNKKV ACGFQTSQGS NILKQ MPEM TSRLLKKFYF WPEARNSAV

UniProtKB: Cell death protein 3

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
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:

3lqq

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 115378
FSC plot (resolution estimation)

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