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- EMDB-36451: The Cryo-EM structure of a heptameric CED-4/CED-3 catalytic complex -

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Basic information

Entry
Database: EMDB / ID: EMD-36451
TitleThe Cryo-EM structure of a heptameric CED-4/CED-3 catalytic complex
Map data
Sample
  • Complex: Heptameric CED-4/CED-3 catalytic complex
    • Protein or peptide: Cell death protein 4
    • Protein or peptide: Cell death protein 4
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsCED-4 / CED-3 catalytic domain / APOPTOSIS
Function / homology
Function and homology information


BH1 domain binding / positive regulation of apoptotic process involved in development / regulation of development, heterochronic / caspase complex / positive regulation of synapse pruning / peptidase activator activity involved in apoptotic process / positive regulation of protein processing / caspase binding / embryonic morphogenesis / apoptotic process involved in development ...BH1 domain binding / positive regulation of apoptotic process involved in development / regulation of development, heterochronic / caspase complex / positive regulation of synapse pruning / peptidase activator activity involved in apoptotic process / positive regulation of protein processing / caspase binding / embryonic morphogenesis / apoptotic process involved in development / negative regulation of execution phase of apoptosis / actin filament depolymerization / activation of cysteine-type endopeptidase activity / embryo development ending in birth or egg hatching / regulation of cell size / muscle cell cellular homeostasis / BH3 domain binding / cysteine-type endopeptidase activator activity involved in apoptotic process / endopeptidase activator activity / regulation of cell adhesion / regulation of protein stability / ADP binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / defense response to Gram-negative bacterium / positive regulation of apoptotic process / apoptotic process / negative regulation of apoptotic process / perinuclear region of cytoplasm / magnesium ion binding / protein-containing complex / mitochondrion / ATP binding / identical protein binding / membrane / nucleus / cytosol
Similarity search - Function
Apoptosis regulator, Ced-4 / Caspase recruitment domain / NB-ARC / NB-ARC domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / 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
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLi Y / Shi Y
Funding support China, 1 items
OrganizationGrant numberCountry
Other private China
CitationJournal: 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.
History
DepositionJun 6, 2023-
Header (metadata) releaseJun 28, 2023-
Map releaseJun 28, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36451.png

Downloads & links

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Map

FileDownload / File: emd_36451.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: 0.021
Minimum - Maximum-0.013534369 - 0.06857926
Average (Standard dev.)0.00022485774 (±0.0023578345)
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_36451_additional_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Half map: #2

Fileemd_36451_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36451_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Heptameric CED-4/CED-3 catalytic complex

EntireName: Heptameric CED-4/CED-3 catalytic complex
Components
  • Complex: Heptameric CED-4/CED-3 catalytic complex
    • Protein or peptide: Cell death protein 4
    • Protein or peptide: Cell death protein 4
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Heptameric CED-4/CED-3 catalytic complex

SupramoleculeName: Heptameric CED-4/CED-3 catalytic complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1
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: 6 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 12.933644 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MLCEIECRAL STAHTRLIHD FEPRDALTYL EGKNIFTEDH SELISKMSTR LERIANFLRI YRRQASELGP LIDFFNYNNQ SHLADFLED YIDFAINEPD LLRPVVIAPQ F

UniProtKB: Cell death protein 4

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Macromolecule #2: Cell death protein 4

MacromoleculeName: Cell death protein 4 / type: protein_or_peptide / ID: 2 / Number of copies: 7 / 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 #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 7 / 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: 7 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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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
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:

3lqq

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 67312
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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