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Open data
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Basic information
Entry | Database: PDB / ID: 5juy | ||||||
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Title | Active human apoptosome with procaspase-9 | ||||||
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![]() | APOPTOSIS / Apaf-1 / programmed cell death / AAA+ ATPase | ||||||
Function / homology | ![]() Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Pyroptosis / Regulation of the apoptosome activity / caspase-9 / Transcriptional activation of mitochondrial biogenesis / response to G1 DNA damage checkpoint signaling / caspase complex / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c ...Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Pyroptosis / Regulation of the apoptosome activity / caspase-9 / Transcriptional activation of mitochondrial biogenesis / response to G1 DNA damage checkpoint signaling / caspase complex / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Formation of apoptosome / regulation of apoptotic DNA fragmentation / Detoxification of Reactive Oxygen Species / apoptosome / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / leukocyte apoptotic process / glial cell apoptotic process / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / Respiratory electron transport / Caspase activation via Dependence Receptors in the absence of ligand / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity / cysteine-type endopeptidase activity involved in apoptotic process / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / AKT phosphorylates targets in the cytosol / mitochondrial electron transport, cytochrome c to oxygen / fibroblast apoptotic process / epithelial cell apoptotic process / platelet formation / mitochondrial electron transport, ubiquinol to cytochrome c / TP53 Regulates Transcription of Caspase Activators and Caspases / Transcriptional Regulation by E2F6 / Constitutive Signaling by AKT1 E17K in Cancer / cysteine-type endopeptidase activator activity involved in apoptotic process / protein maturation / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / signal transduction in response to DNA damage / cellular response to dexamethasone stimulus / : / response to nutrient / forebrain development / cardiac muscle cell apoptotic process / cellular response to transforming growth factor beta stimulus / enzyme activator activity / heat shock protein binding / intrinsic apoptotic signaling pathway / positive regulation of apoptotic signaling pathway / kidney development / neural tube closure / response to ischemia / NOD1/2 Signaling Pathway / mitochondrial intermembrane space / protein processing / activation of cysteine-type endopeptidase activity involved in apoptotic process / ADP binding / SH3 domain binding / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to UV / positive regulation of neuron apoptotic process / response to estradiol / nervous system development / peptidase activity / secretory granule lumen / neuron apoptotic process / regulation of apoptotic process / ficolin-1-rich granule lumen / response to lipopolysaccharide / cell differentiation / response to hypoxia / electron transfer activity / positive regulation of apoptotic process / cysteine-type endopeptidase activity / nucleotide binding / DNA damage response / heme binding / Neutrophil degranulation / protein kinase binding / apoptotic process / protein-containing complex / mitochondrion / extracellular exosome / extracellular region / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||
![]() | Cheng, T.C. / Hong, C. / Akey, I.V. / Yuan, S. / Akey, C.W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A near atomic structure of the active human apoptosome. Authors: Tat Cheung Cheng / Chuan Hong / Ildikó V Akey / Shujun Yuan / Christopher W Akey / ![]() Abstract: In response to cell death signals, an active apoptosome is assembled from Apaf-1 and procaspase-9 (pc-9). Here we report a near atomic structure of the active human apoptosome determined by cryo- ...In response to cell death signals, an active apoptosome is assembled from Apaf-1 and procaspase-9 (pc-9). Here we report a near atomic structure of the active human apoptosome determined by cryo-electron microscopy. The resulting model gives insights into cytochrome c binding, nucleotide exchange and conformational changes that drive assembly. During activation an acentric disk is formed on the central hub of the apoptosome. This disk contains four Apaf-1/pc-9 CARD pairs arranged in a shallow spiral with the fourth pc-9 CARD at lower occupancy. On average, Apaf-1 CARDs recruit 3 to 5 pc-9 molecules to the apoptosome and one catalytic domain may be parked on the hub, when an odd number of zymogens are bound. This suggests a stoichiometry of one or at most, two pc-9 dimers per active apoptosome. Thus, our structure provides a molecular framework to understand the role of the apoptosome in programmed cell death and disease. | ||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.6 MB | Display | ![]() |
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PDB format | ![]() | 1.3 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8178MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 142023.672 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Details: without N-terminal CARDs / Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 11595.392 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 11140.723 Da / Num. of mol.: 4 / Fragment: N-terminal caspase recognition domain Source method: isolated from a genetically manipulated source Details: N-terminal caspase recognition domain (CARD) of procaspase-9 Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: P55211, caspase-9 #4: Chemical | ChemComp-DTP / #5: Chemical | ChemComp-HEC / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Active complex of Apaf-1, cytochrome c and pro-caspase 9 Type: COMPLEX Details: Complex stoichiometry: 4 full length Apaf-1 molecules with ordered N-terminal CARDs, 3 truncated Apaf-1 molecules without CARDs, 7 cytochrome c molecules and 4 N-terminal CARDs from procaspase-9 Entity ID: #1-#4 / Source: RECOMBINANT | |||||||||||||||||||||||||||||||||||
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Molecular weight | Value: 1.3 MDa / Experimental value: NO | |||||||||||||||||||||||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | |||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 / Details: Buffer A | |||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3 | |||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS Details: data collected with a Cs aberration corrector and a GIF energy filter with a slit width of 20 eV. |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1500 nm / Cs: 0.01 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 0.3 sec. / Electron dose: 1.8 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1991 |
EM imaging optics | Energyfilter name: GIF |
Image scans | Width: 7676 / Height: 7420 / Movie frames/image: 23 / Used frames/image: 2-23 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 134970 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C7 (7 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92867 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL Details: Initial rigid body fitting with Chimera with a previously published starting model (PDB 3J2T), molecular dynamics flexible fitting with MDFF and real space density refinement with Phenix |