+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38462 | |||||||||
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Title | Cryo-EM structure of mouse BIRC6, Half map of the core region | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Inhibitor of apoptosis protein / BIRC6 / Smac / APOPTOSIS | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Liu S / Jiang T / Bu F / Zhao J / Wang G / Li N / Gao N / Qiu X | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Molecular mechanisms underlying the BIRC6-mediated regulation of apoptosis and autophagy. Authors: Shuo-Shuo Liu / Tian-Xia Jiang / Fan Bu / Ji-Lan Zhao / Guang-Fei Wang / Guo-Heng Yang / Jie-Yan Kong / Yun-Fan Qie / Pei Wen / Li-Bin Fan / Ning-Ning Li / Ning Gao / Xiao-Bo Qiu / Abstract: Procaspase 9 is the initiator caspase for apoptosis, but how its levels and activities are maintained remains unclear. The gigantic Inhibitor-of-Apoptosis Protein BIRC6/BRUCE/Apollon inhibits both ...Procaspase 9 is the initiator caspase for apoptosis, but how its levels and activities are maintained remains unclear. The gigantic Inhibitor-of-Apoptosis Protein BIRC6/BRUCE/Apollon inhibits both apoptosis and autophagy by promoting ubiquitylation of proapoptotic factors and the key autophagic protein LC3, respectively. Here we show that BIRC6 forms an anti-parallel U-shaped dimer with multiple previously unannotated domains, including a ubiquitin-like domain, and the proapoptotic factor Smac/DIABLO binds BIRC6 in the central cavity. Notably, Smac outcompetes the effector caspase 3 and the pro-apoptotic protease HtrA2, but not procaspase 9, for binding BIRC6 in cells. BIRC6 also binds LC3 through its LC3-interacting region, probably following dimer disruption of this BIRC6 region. Mutation at LC3 ubiquitylation site promotes autophagy and autophagic degradation of BIRC6. Moreover, induction of autophagy promotes autophagic degradation of BIRC6 and caspase 9, but not of other effector caspases. These results are important to understand how the balance between apoptosis and autophagy is regulated under pathophysiological conditions. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38462.map.gz | 2.7 MB | EMDB map data format | |
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Header (meta data) | emd-38462-v30.xml emd-38462.xml | 12.4 KB 12.4 KB | Display Display | EMDB header |
Images | emd_38462.png | 130.8 KB | ||
Masks | emd_38462_msk_1.map | 30.5 MB | Mask map | |
Filedesc metadata | emd-38462.cif.gz | 4 KB | ||
Others | emd_38462_half_map_1.map.gz emd_38462_half_map_2.map.gz | 23.3 MB 23.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38462 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38462 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_38462.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.37 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_38462_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_38462_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_38462_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Baculoviral IAP repeat-containing protein 6, Dimer
Entire | Name: Baculoviral IAP repeat-containing protein 6, Dimer |
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Components |
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-Supramolecule #1: Baculoviral IAP repeat-containing protein 6, Dimer
Supramolecule | Name: Baculoviral IAP repeat-containing protein 6, Dimer / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.0 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 68.4 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 308000 |