+Open data
-Basic information
Entry | Database: PDB / ID: 5wve | ||||||||||||
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Title | Apaf-1-Caspase-9 holoenzyme | ||||||||||||
Components |
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Keywords | APOPTOSIS / apoptosis holoenzyme | ||||||||||||
Function / homology | Function and homology information caspase-9 / response to G1 DNA damage checkpoint signaling / caspase complex / 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 / leukocyte apoptotic process ...caspase-9 / response to G1 DNA damage checkpoint signaling / caspase complex / 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 / leukocyte apoptotic process / glial cell apoptotic process / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / positive regulation of cysteine-type endopeptidase activity / 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 / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / 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 / lipid binding / heme binding / Neutrophil degranulation / protein kinase binding / apoptotic process / protein-containing complex / mitochondrion / proteolysis / extracellular exosome / extracellular region / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Equus caballus (horse) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å | ||||||||||||
Authors | Li, Y. / Zhou, M. / Hu, Q. / Shi, Y. | ||||||||||||
Funding support | China, United Kingdom, 3items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2017 Title: Mechanistic insights into caspase-9 activation by the structure of the apoptosome holoenzyme. Authors: Yini Li / Mengying Zhou / Qi Hu / Xiao-Chen Bai / Weiyun Huang / Sjors H W Scheres / Yigong Shi / Abstract: Mammalian intrinsic apoptosis requires activation of the initiator caspase-9, which then cleaves and activates the effector caspases to execute cell killing. The heptameric Apaf-1 apoptosome is ...Mammalian intrinsic apoptosis requires activation of the initiator caspase-9, which then cleaves and activates the effector caspases to execute cell killing. The heptameric Apaf-1 apoptosome is indispensable for caspase-9 activation by together forming a holoenzyme. The molecular mechanism of caspase-9 activation remains largely enigmatic. Here, we report the cryoelectron microscopy (cryo-EM) structure of an apoptotic holoenzyme and structure-guided biochemical analyses. The caspase recruitment domains (CARDs) of Apaf-1 and caspase-9 assemble in two different ways: a 4:4 complex docks onto the central hub of the apoptosome, and a 2:1 complex binds the periphery of the central hub. The interface between the CARD complex and the central hub is required for caspase-9 activation within the holoenzyme. Unexpectedly, the CARD of free caspase-9 strongly inhibits its proteolytic activity. These structural and biochemical findings demonstrate that the apoptosome activates caspase-9 at least in part through sequestration of the inhibitory CARD domain. | ||||||||||||
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 | 5wve.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5wve.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 5wve.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wve_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 5wve_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 5wve_validation.xml.gz | 377 KB | Display | |
Data in CIF | 5wve_validation.cif.gz | 530.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/5wve ftp://data.pdbj.org/pub/pdb/validation_reports/wv/5wve | HTTPS FTP |
-Related structure data
Related structure data | 6690MC 6691C 6692C 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
-Apoptotic protease-activating factor ... , 2 types, 13 molecules ACEGIKMOPQRWX
#1: Protein | Mass: 142023.672 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APAF1, KIAA0413 Production host: Insect cell expression vector pTIE1 (others) References: UniProt: O14727 #3: Protein | Mass: 11575.185 Da / Num. of mol.: 6 / Fragment: CARD domain, UNP residues 1-102 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APAF1, KIAA0413 Production host: Insect cell expression vector pTIE1 (others) References: UniProt: O14727 |
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-Protein , 2 types, 12 molecules BDFHJLNSTUVY
#2: Protein | Mass: 11856.793 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Gene: CYCS, CYC / Production host: Bacteria (eubacteria) / References: UniProt: P00004 #4: Protein | Mass: 11698.449 Da / Num. of mol.: 5 / Fragment: CARD domain, UNP residues 1-100 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Bacteria (eubacteria) / References: UniProt: A8K7U6, UniProt: P55211*PLUS |
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-Non-polymers , 3 types, 21 molecules
#5: Chemical | ChemComp-DTP / #6: Chemical | ChemComp-MG / #7: 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
Component |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 32 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 240130 / Symmetry type: POINT |