+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3918 | |||||||||
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Title | Recombinant human Bri2 BRICHOS domain, oligomeric state | |||||||||
Map data | Negative stain 3D density map of the Bri2 Brichos domain in its oligomeric state, Molecular wieght, 370 kDaMethod: Single particle TEM | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 16.5 Å | |||||||||
Authors | Hebert H / Johansson J / Nilsson HE / Koeck PJB / Chen G | |||||||||
Citation | Journal: Nat Commun / Year: 2017 Title: Bri2 BRICHOS client specificity and chaperone activity are governed by assembly state. Authors: Gefei Chen / Axel Abelein / Harriet E Nilsson / Axel Leppert / Yuniesky Andrade-Talavera / Simone Tambaro / Lovisa Hemmingsson / Firoz Roshan / Michael Landreh / Henrik Biverstål / Philip J ...Authors: Gefei Chen / Axel Abelein / Harriet E Nilsson / Axel Leppert / Yuniesky Andrade-Talavera / Simone Tambaro / Lovisa Hemmingsson / Firoz Roshan / Michael Landreh / Henrik Biverstål / Philip J B Koeck / Jenny Presto / Hans Hebert / André Fisahn / Jan Johansson / Abstract: Protein misfolding and aggregation is increasingly being recognized as a cause of disease. In Alzheimer's disease the amyloid-β peptide (Aβ) misfolds into neurotoxic oligomers and assembles into ...Protein misfolding and aggregation is increasingly being recognized as a cause of disease. In Alzheimer's disease the amyloid-β peptide (Aβ) misfolds into neurotoxic oligomers and assembles into amyloid fibrils. The Bri2 protein associated with Familial British and Danish dementias contains a BRICHOS domain, which reduces Aβ fibrillization as well as neurotoxicity in vitro and in a Drosophila model, but also rescues proteins from irreversible non-fibrillar aggregation. How these different activities are mediated is not known. Here we show that Bri2 BRICHOS monomers potently prevent neuronal network toxicity of Aβ, while dimers strongly suppress Aβ fibril formation. The dimers assemble into high-molecular-weight oligomers with an apparent two-fold symmetry, which are efficient inhibitors of non-fibrillar protein aggregation. These results indicate that Bri2 BRICHOS affects qualitatively different aspects of protein misfolding and toxicity via different quaternary structures, suggesting a means to generate molecular chaperone diversity. | |||||||||
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_3918.map.gz | 1.2 MB | EMDB map data format | |
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Header (meta data) | emd-3918-v30.xml emd-3918.xml | 13.4 KB 13.4 KB | Display Display | EMDB header |
Images | emd_3918.png | 132.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3918 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3918 | 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_3918.map.gz / Format: CCP4 / Size: 4.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Negative stain 3D density map of the Bri2 Brichos domain in its oligomeric state, Molecular wieght, 370 kDaMethod: Single particle TEM | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.076 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 : Oligomeric Bri2 BRICHOS
Entire | Name: Oligomeric Bri2 BRICHOS |
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Components |
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-Supramolecule #1: Oligomeric Bri2 BRICHOS
Supramolecule | Name: Oligomeric Bri2 BRICHOS / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Experimental: 370 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: Shuttle T7 / Recombinant plasmid: pET |
-Macromolecule #1: Bri2 BRICHOS domain
Macromolecule | Name: Bri2 BRICHOS domain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GSQTIEENIK IFEEEEVEFS VPVPEFADDP ANIVHDFNKK LTAYLDLNLD KCYVIPLNTS IVMPPRNLLE LLINIKAGTY LPQSYLIHEH MVITDRIENI DHLGFFIYRL CHDKETYKL |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.047 mg/mL |
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Buffer | pH: 8 / Component - Concentration: 20.0 mM / Component - Formula: C2H7NO2 / Component - Name: Ammonium acetate |
Staining | Type: NEGATIVE / Material: Uranyl Acetate / Details: 2% Uranyl Acetate |
Grid | Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.005 kPa |
Details | Purified fraction with protein was immediately stored on ice followed by grid preparation. |
-Electron microscopy
Microscope | JEOL 2100F |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 2.1 µm / Calibrated defocus min: 0.8 µm / Calibrated magnification: 61680 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal magnification: 60000 |
Sample stage | Specimen holder model: JEOL |
Details | per frame =1.44 e/A2 |
Image recording | Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 5120 pixel / Digitization - Dimensions - Height: 3840 pixel / Number real images: 24 / Average exposure time: 2.0 sec. / Average electron dose: 57.5 e/Å2 Details: Negative stain images were collected in movie-mode at 20 frames per second. For each exposure, the comprised frames were drift corrected using the DE_process_frames-2.7.1.py script |
-Image processing
Particle selection | Number selected: 3000 Details: negative monitor contrast faciliated particle picking |
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CTF correction | Software - Name: EMAN2 (ver. 2.12) Details: For low resolution data EMAN2 use a 1D structure factor during the CTF procedure |
Startup model | Type of model: OTHER Details: The initial model was based on a subset of class-averages representing different views |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: EMAN2 (ver. 2.12) |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: EMAN2 (ver. 2.12) |
Final reconstruction | Applied symmetry - Point group: D2 (2x2 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 16.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 (ver. 2.12) / Number images used: 2718 |