+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8178 | |||||||||
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Title | Active human apoptosome with procaspase-9 | |||||||||
Map data | Active human apoptosome with procaspase-9 | |||||||||
Sample |
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Function / homology | Function and homology information 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 | Homo sapiens (human) / Bovine (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Cheng TC / Hong C / Akey IV / Yuan S / Akey CW | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Elife / Year: 2016 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8178.map.gz | 8.6 MB | EMDB map data format | |
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Header (meta data) | emd-8178-v30.xml emd-8178.xml | 21.4 KB 21.4 KB | Display Display | EMDB header |
Images | emd_8178.png | 81.7 KB | ||
Others | emd_8178_additional.map.gz | 6.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8178 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8178 | HTTPS FTP |
-Validation report
Summary document | emd_8178_validation.pdf.gz | 344.4 KB | Display | EMDB validaton report |
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Full document | emd_8178_full_validation.pdf.gz | 344 KB | Display | |
Data in XML | emd_8178_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | emd_8178_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8178 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8178 | HTTPS FTP |
-Related structure data
Related structure data | 5juyMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8178.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Active human apoptosome with procaspase-9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.368 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Active human apoptosome with procaspase-9
File | emd_8178_additional.map | ||||||||||||
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Annotation | Active human apoptosome with procaspase-9 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Active complex of Apaf-1, cytochrome c and pro-caspase 9
Entire | Name: Active complex of Apaf-1, cytochrome c and pro-caspase 9 |
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Components |
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-Supramolecule #1: Active complex of Apaf-1, cytochrome c and pro-caspase 9
Supramolecule | Name: Active complex of Apaf-1, cytochrome c and pro-caspase 9 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 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 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant plasmid: pFast-Bac |
Molecular weight | Theoretical: 1.3 MDa |
-Macromolecule #1: Apoptotic protease-activating factor 1
Macromolecule | Name: Apoptotic protease-activating factor 1 / type: protein_or_peptide / ID: 1 / Details: without N-terminal CARDs / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 142.023672 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MDAKARNCLL QHREALEKDI KTSYIMDHMI SDGFLTISEE EKVRNEPTQQ QRAAMLIKMI LKKDNDSYVS FYNALLHEGY KDLAALLHD GIPVVSSSSG KDSVSGITSY VRTVLCEGGV PQRPVVFVTR KKLVNAIQQK LSKLKGEPGW VTIHGMAGCG K SVLAAEAV ...String: MDAKARNCLL QHREALEKDI KTSYIMDHMI SDGFLTISEE EKVRNEPTQQ QRAAMLIKMI LKKDNDSYVS FYNALLHEGY KDLAALLHD GIPVVSSSSG KDSVSGITSY VRTVLCEGGV PQRPVVFVTR KKLVNAIQQK LSKLKGEPGW VTIHGMAGCG K SVLAAEAV RDHSLLEGCF PGGVHWVSVG KQDKSGLLMK LQNLCTRLDQ DESFSQRLPL NIEEAKDRLR ILMLRKHPRS LL ILDDVWD SWVLKAFDSQ CQILLTTRDK SVTDSVMGPK YVVPVESSLG KEKGLEILSL FVNMKKADLP EQAHSIIKEC KGS PLVVSL IGALLRDFPN RWEYYLKQLQ NKQFKRIRKS SSYDYEALDE AMSISVEMLR EDIKDYYTDL SILQKDVKVP TKVL CILWD METEEVEDIL QEFVNKSLLF CDRNGKSFRY YLHDLQVDFL TEKNCSQLQD LHKKIITQFQ RYHQPHTLSP DQEDC MYWY NFLAYHMASA KMHKELCALM FSLDWIKAKT ELVGPAHLIH EFVEYRHILD EKDCAVSENF QEFLSLNGHL LGRQPF PNI VQLGLCEPET SEVYQQAKLQ AKQEVDNGML YLEWINKKNI TNLSRLVVRP HTDAVYHACF SEDGQRIASC GADKTLQ VF KAETGEKLLE IKAHEDEVLC CAFSTDDRFI ATCSVDKKVK IWNSMTGELV HTYDEHSEQV NCCHFTNSSH HLLLATGS S DCFLKLWDLN QKECRNTMFG HTNSVNHCRF SPDDKLLASC SADGTLKLWD ATSANERKSI NVKQFFLNLE DPQEDMEVI VKCCSWSADG ARIMVAAKNK IFLFDIHTSG LLGEIHTGHH STIQYCDFSP QNHLAVVALS QYCVELWNTD SRSKVADCRG HLSWVHGVM FSPDGSSFLT SSDDQTIRLW ETKKVCKNSA VMLKQEVDVV FQENEVMVLA VDHIRRLQLI NGRTGQIDYL T EAQVSCCC LSPHLQYIAF GDENGAIEIL ELVNNRIFQS RFQHKKTVWH IQFTADEKTL ISSSDDAEIQ VWNWQLDKCI FL RGHQETV KDFRLLKNSR LLSWSFDGTV KVWNIITGNK EKDFVCHQGT VLSCDISHDA TKFSSTSADK TAKIWSFDLL LPL HELRGH NGCVRCSAFS VDSTLLATGD DNGEIRIWNV SNGELLHLCA PLSEEGAATH GGWVTDLCFS PDGKMLISAG GYIK WWNVV TGESSQTFYT NGTNLKKIHV SPDFKTYVTV DNLGILYILQ TLE |
-Macromolecule #2: Cytochrome c
Macromolecule | Name: Cytochrome c / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Bovine (cattle) |
Molecular weight | Theoretical: 11.595392 KDa |
Sequence | String: GDVEKGKKIF VQKCAQCHTV EKGGKHKTGP NLHGLFGRKT GQAPGFSYTD ANKNKGITWG EETLMEYLEN PKKYIPGTKM IFAGIKKKG EREDLIAYLK KATNE |
-Macromolecule #3: Caspase-9
Macromolecule | Name: Caspase-9 / type: protein_or_peptide / ID: 3 Details: N-terminal caspase recognition domain (CARD) of procaspase-9 Number of copies: 4 / Enantiomer: LEVO / EC number: caspase-9 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.140723 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MDEADRRLLR RCRLRLVEEL QVDQLWDALL SRELFRPHMI EDIQRAGSGS RRDQARQLII DLETRGSQAL PLFISCLEDT GQDMLASFL RTNRQA |
-Macromolecule #4: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
Macromolecule | Name: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 7 / Formula: DTP |
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Molecular weight | Theoretical: 491.182 Da |
Chemical component information | ChemComp-DTP: |
-Macromolecule #5: HEME C
Macromolecule | Name: HEME C / type: ligand / ID: 5 / Number of copies: 7 / Formula: HEC |
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Molecular weight | Theoretical: 618.503 Da |
Chemical component information | ChemComp-HEC: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4.0 mg/mL | |||||||||||||||||||||
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Buffer | pH: 7.5 Component:
Details: Buffer A | |||||||||||||||||||||
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF |
Details | data collected with a Cs aberration corrector and a GIF energy filter with a slit width of 20 eV. |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7676 pixel / Digitization - Dimensions - Height: 7420 pixel / Digitization - Frames/image: 2-23 / Number grids imaged: 1 / Number real images: 1991 / Average exposure time: 0.3 sec. / Average electron dose: 1.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
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 |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | PDB-5juy: |