+Open data
-Basic information
Entry | Database: PDB / ID: 3jbt | ||||||
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Title | Atomic structure of the Apaf-1 apoptosome | ||||||
Components |
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Keywords | APOPTOSIS / Apoptosome / cryo-EM structure / Apaf-1 | ||||||
Function / homology | Function and homology information response to G1 DNA damage checkpoint signaling / cytochrome c-heme linkage / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Formation of apoptosome / regulation of apoptotic DNA fragmentation / apoptosome / cytochrome complex / positive regulation of cysteine-type endopeptidase activity / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity ...response to G1 DNA damage checkpoint signaling / cytochrome c-heme linkage / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Formation of apoptosome / regulation of apoptotic DNA fragmentation / apoptosome / cytochrome complex / positive regulation of cysteine-type endopeptidase activity / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / TP53 Regulates Transcription of Caspase Activators and Caspases / Transcriptional Regulation by E2F6 / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / cysteine-type endopeptidase activator activity involved in apoptotic process / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / : / response to nutrient / forebrain development / cardiac muscle cell apoptotic process / cellular response to transforming growth factor beta stimulus / heat shock protein binding / intrinsic apoptotic signaling pathway / positive regulation of apoptotic signaling pathway / kidney development / neural tube closure / mitochondrial intermembrane space / activation of cysteine-type endopeptidase activity involved in apoptotic process / ADP binding / nervous system development / secretory granule lumen / neuron apoptotic process / regulation of apoptotic process / ficolin-1-rich granule lumen / cell differentiation / response to hypoxia / electron transfer activity / positive regulation of apoptotic process / nucleotide binding / lipid binding / heme binding / Neutrophil degranulation / apoptotic process / protein-containing complex / extracellular exosome / extracellular region / ATP binding / identical protein binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Equus caballus (horse) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
Authors | Zhou, M. / Li, Y. / Hu, Q. / Bai, X. / Huang, W. / Yan, C. / Scheres, S.H.W. / Shi, Y. | ||||||
Citation | Journal: Genes Dev / Year: 2015 Title: Atomic structure of the apoptosome: mechanism of cytochrome c- and dATP-mediated activation of Apaf-1. Authors: Mengying Zhou / Yini Li / Qi Hu / Xiao-Chen Bai / Weiyun Huang / Chuangye Yan / Sjors H W Scheres / Yigong Shi / Abstract: The apoptotic protease-activating factor 1 (Apaf-1) controls the onset of many known forms of intrinsic apoptosis in mammals. Apaf-1 exists in normal cells as an autoinhibited monomer. Upon binding ...The apoptotic protease-activating factor 1 (Apaf-1) controls the onset of many known forms of intrinsic apoptosis in mammals. Apaf-1 exists in normal cells as an autoinhibited monomer. Upon binding to cytochrome c and dATP, Apaf-1 oligomerizes into a heptameric complex known as the apoptosome, which recruits and activates cell-killing caspases. Here we present an atomic structure of an intact mammalian apoptosome at 3.8 Å resolution, determined by single-particle, cryo-electron microscopy (cryo-EM). Structural analysis, together with structure-guided biochemical characterization, uncovered how cytochrome c releases the autoinhibition of Apaf-1 through specific interactions with the WD40 repeats. Structural comparison with autoinhibited Apaf-1 revealed how dATP binding triggers a set of conformational changes that results in the formation of the apoptosome. Together, these results constitute the molecular mechanism of cytochrome c- and dATP-mediated activation of Apaf-1. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3jbt.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3jbt.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 3jbt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jbt_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 3jbt_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 3jbt_validation.xml.gz | 339.9 KB | Display | |
Data in CIF | 3jbt_validation.cif.gz | 478 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/3jbt ftp://data.pdbj.org/pub/pdb/validation_reports/jb/3jbt | HTTPS FTP |
-Related structure data
Related structure data | 6480MC 6481MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 143647.344 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APAF1, KIAA0413 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O14727 #2: Protein | Mass: 11856.793 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P00004 #3: Chemical | ChemComp-DTP / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-HEM / |
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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 |
-Sample preparation
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Buffer solution | Name: 20 mM HEPES (pH 7.5), 10 mM KCl, 1.5 mM MgCl2, 1 mM EDTA, 1 mM DTT pH: 7.5 Details: 20 mM HEPES (pH 7.5), 10 mM KCl, 1.5 mM MgCl2, 1 mM EDTA, 1 mM DTT | ||||||||||||||||||||
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Details: 400-mesh Cu R 1.2/1.3 grids | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Method: Blot for 2.5 seconds before plunging |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Jan 10, 2015 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1400 nm / Cs: 2 mm / Camera length: 0 mm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K2 (4k x 4k) |
-Processing
EM software |
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Symmetry | Point symmetry: C7 (7 fold cyclic) | ||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 134919 / Actual pixel size: 1.32 Å / Details: (Single particle--Applied symmetry: C7) / Symmetry type: POINT | ||||||||||||
Atomic model building |
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Atomic model building |
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Refinement step | Cycle: LAST
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