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- EMDB-1614: Globular tetramers of beta-2-microglobulin assemble into elaborat... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1614 | |||||||||
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Title | Globular tetramers of beta-2-microglobulin assemble into elaborate amyloid fibrils | |||||||||
![]() | Surface view of an B-type map from beta-2-microglobulin | |||||||||
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Function / homology | ![]() ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | helical reconstruction / ![]() | |||||||||
![]() | White HE / Hodgkinson JL / Jahn TR / Cohen-Krausz S / Gosal WS / Muller S / Orlova EV / Radford SE / Saibil HR | |||||||||
![]() | ![]() Title: Globular tetramers of beta(2)-microglobulin assemble into elaborate amyloid fibrils. Authors: Helen E White / Julie L Hodgkinson / Thomas R Jahn / Sara Cohen-Krausz / Walraj S Gosal / Shirley Müller / Elena V Orlova / Sheena E Radford / Helen R Saibil / ![]() Abstract: Amyloid fibrils are ordered polymers in which constituent polypeptides adopt a non-native fold. Despite their importance in degenerative human diseases, the overall structure of amyloid fibrils ...Amyloid fibrils are ordered polymers in which constituent polypeptides adopt a non-native fold. Despite their importance in degenerative human diseases, the overall structure of amyloid fibrils remains unknown. High-resolution studies of model peptide assemblies have identified residues forming cross-beta-strands and have revealed some details of local beta-strand packing. However, little is known about the assembly contacts that define the fibril architecture. Here we present a set of three-dimensional structures of amyloid fibrils formed from full-length beta(2)-microglobulin, a 99-residue protein involved in clinical amyloidosis. Our cryo-electron microscopy maps reveal a hierarchical fibril structure built from tetrameric units of globular density, with at least three different subunit interfaces in this homopolymeric assembly. These findings suggest a more complex superstructure for amyloid than hitherto suspected and prompt a re-evaluation of the defining features of the amyloid fold. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 1.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.9 KB 9.9 KB | Display Display | ![]() |
Images | ![]() | 737.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Surface view of an B-type map from beta-2-microglobulin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : beta-2-microglobulin
Entire | Name: beta-2-microglobulin![]() |
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Components |
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-Supramolecule #1000: beta-2-microglobulin
Supramolecule | Name: beta-2-microglobulin / type: sample / ID: 1000 / Number unique components: 1 |
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Molecular weight | Experimental: 10 KDa |
-Macromolecule #1: beta-2-microglobulin
Macromolecule | Name: beta-2-microglobulin / type: protein_or_peptide / ID: 1 / Name.synonym: beta-2-microglobulin / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 10 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | GO: MHC class I protein complex / InterPro: ![]() |
-Experimental details
-Structure determination
Method | ![]() |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 2.5 / Details: 25 mM sodium phosphate, 25 mM sodium acetate |
Grid | Details: holey carbon grids |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: manual plunger |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder: side entry / Specimen holder model: GATAN LIQUID NITROGEN |
Temperature | Min: 100 K |
Details | Low dose |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 85 / Bits/pixel: 8 |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
CTF correction | Details: Phase flipping |
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Final reconstruction | Applied symmetry - Helical parameters - Δz: 52.5 Å Applied symmetry - Helical parameters - Δ&Phi: 7.01 ° Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER Details: Maps were calculated for each class as each class had a different pitch. |