+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8993 | |||||||||
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Title | Class III PI3K Complex 2 with inhibitor Rubicon | |||||||||
Map data | CryoEM map between 6-8 angstroms of the Class III PI3K Complex 2, bound to an inhibitor from Rubicon | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.8 Å | |||||||||
Authors | Young LN / Morris KL / Hurley JH | |||||||||
Citation | Journal: Mol Cell / Year: 2019 Title: Bidirectional Control of Autophagy by BECN1 BARA Domain Dynamics. Authors: Chunmei Chang / Lindsey N Young / Kyle L Morris / Sören von Bülow / Johannes Schöneberg / Hitomi Yamamoto-Imoto / Yukako Oe / Kentaro Yamamoto / Shuhei Nakamura / Goran Stjepanovic / ...Authors: Chunmei Chang / Lindsey N Young / Kyle L Morris / Sören von Bülow / Johannes Schöneberg / Hitomi Yamamoto-Imoto / Yukako Oe / Kentaro Yamamoto / Shuhei Nakamura / Goran Stjepanovic / Gerhard Hummer / Tamotsu Yoshimori / James H Hurley / Abstract: Membrane targeting of the BECN1-containing class III PI 3-kinase (PI3KC3) complexes is pivotal to the regulation of autophagy. The interaction of PI3KC3 complex II and its ubiquitously expressed ...Membrane targeting of the BECN1-containing class III PI 3-kinase (PI3KC3) complexes is pivotal to the regulation of autophagy. The interaction of PI3KC3 complex II and its ubiquitously expressed inhibitor, Rubicon, was mapped to the first β sheet of the BECN1 BARA domain and the UVRAG BARA2 domain by hydrogen-deuterium exchange and cryo-EM. These data suggest that the BARA β sheet 1 unfolds to directly engage the membrane. This mechanism was confirmed using protein engineering, giant unilamellar vesicle assays, and molecular simulations. Using this mechanism, a BECN1 β sheet-1 derived peptide activates both PI3KC3 complexes I and II, while HIV-1 Nef inhibits complex II. These data reveal how BECN1 switches on and off PI3KC3 binding to membranes. The observations explain how PI3KC3 inhibition by Rubicon, activation by autophagy-inducing BECN1 peptides, and inhibition by HIV-1 Nef are mediated by the switchable ability of the BECN1 BARA domain to partially unfold and insert into membranes. | |||||||||
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_8993.map.gz | 155.6 MB | EMDB map data format | |
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Header (meta data) | emd-8993-v30.xml emd-8993.xml | 10 KB 10 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8993_fsc.xml | 12.6 KB | Display | FSC data file |
Images | emd_8993.png | 180.2 KB | ||
Masks | emd_8993_msk_1.map | 166.4 MB | Mask map | |
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8993 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8993 | 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_8993.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CryoEM map between 6-8 angstroms of the Class III PI3K Complex 2, bound to an inhibitor from Rubicon | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_8993_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Core scaffold of PI3K Complex 2 bound to inhibitor Rubicon
Entire | Name: Core scaffold of PI3K Complex 2 bound to inhibitor Rubicon |
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Components |
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-Supramolecule #1: Core scaffold of PI3K Complex 2 bound to inhibitor Rubicon
Supramolecule | Name: Core scaffold of PI3K Complex 2 bound to inhibitor Rubicon type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant strain: HEK 293 GNTI |
Molecular weight | Theoretical: 360 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK IV |
Details | This sample was monodisperse. |
-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 |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 59.7 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |