+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9011 | |||||||||
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Title | Bax with activating Bid peptide inserted into nanodisc. | |||||||||
Map data | Bax with activating Bid peptide inserted in nanodiscs | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 28.0 Å | |||||||||
Authors | Volkmann N / Hanein D | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Structure / Year: 2019 Title: Biophysical Characterization of a Nanodisc with and without BAX: An Integrative Study Using Molecular Dynamics Simulations and Cryo-EM. Authors: Cesar A López / Mark F Swift / Xiao-Ping Xu / Dorit Hanein / Niels Volkmann / S Gnanakaran / Abstract: B cell lymphoma-2-associated X protein (BAX) plays a pivotal role in triggering cell apoptosis by permeabilizing the mitochondrial outer membrane. Contrary to previous findings, recent electron ...B cell lymphoma-2-associated X protein (BAX) plays a pivotal role in triggering cell apoptosis by permeabilizing the mitochondrial outer membrane. Contrary to previous findings, recent electron microscopy (EM) experiments showed that BAX monomers are able to perturb phospholipid nanodiscs (NDs) by forming lipidic pores. Here, we provide structural and thermodynamic interpretation of such data using multiscale resolution molecular dynamics (MD) simulations. Our results suggest that BAX is able to disrupt the stability, lateral packing and enhance the desorption propensity of the lipids in the ND, resulting in the formation of a stable toroidal-like pore. These findings prompted to re-evaluate the previously reported cryo-EM data to generate an improved reconstruction, thereby allowing for a more accurate localization of BAX in the EM map. We conclude that the reduced stability of the BAX-embedded ND eliminates the necessity of forming active BAX oligomers for its disruption. | |||||||||
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_9011.map.gz | 45.4 KB | EMDB map data format | |
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Header (meta data) | emd-9011-v30.xml emd-9011.xml | 7.7 KB 7.7 KB | Display Display | EMDB header |
Images | emd_9011.png | 66.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9011 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9011 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_9011.map.gz / Format: CCP4 / Size: 251 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Bax with activating Bid peptide inserted in nanodiscs | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6.76 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Complex of Bax and activating Bid peptide inserted in nanodisc
Entire | Name: Complex of Bax and activating Bid peptide inserted in nanodisc |
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Components |
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-Supramolecule #1: Complex of Bax and activating Bid peptide inserted in nanodisc
Supramolecule | Name: Complex of Bax and activating Bid peptide inserted in nanodisc type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: KODAK SO-163 FILM / Average electron dose: 25.0 e/Å2 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: EMAN2 |
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Startup model | Type of model: OTHER Details: Previously obtained reconstructions of the same sample |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: EMAN2 |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: EMAN2 |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 4312 |