[English] 日本語
Yorodumi- EMDB-1614: Globular tetramers of beta-2-microglobulin assemble into elaborat... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1614 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Globular tetramers of beta-2-microglobulin assemble into elaborate amyloid fibrils | |||||||||
Map data | Surface view of an B-type map from beta-2-microglobulin | |||||||||
Sample |
| |||||||||
Keywords | protein misfolding / amyloid / cryo-EM / 3D reconstruction / STEM | |||||||||
Function / homology | Beta-2-Microglobulin / MHC class I protein complex Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 25.0 Å | |||||||||
Authors | White HE / Hodgkinson JL / Jahn TR / Cohen-Krausz S / Gosal WS / Muller S / Orlova EV / Radford SE / Saibil HR | |||||||||
Citation | Journal: J Mol Biol / Year: 2009 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1614.map.gz | 1.7 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-1614-v30.xml emd-1614.xml | 9.9 KB 9.9 KB | Display Display | EMDB header |
Images | 1614.tif | 737.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1614 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1614 | HTTPS FTP |
-Validation report
Summary document | emd_1614_validation.pdf.gz | 208.8 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_1614_full_validation.pdf.gz | 208 KB | Display | |
Data in XML | emd_1614_validation.xml.gz | 5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1614 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1614 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_1614.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : beta-2-microglobulin
Entire | Name: beta-2-microglobulin |
---|---|
Components |
|
-Supramolecule #1000: beta-2-microglobulin
Supramolecule | Name: beta-2-microglobulin / type: sample / ID: 1000 / Number unique components: 1 |
---|---|
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 |
---|---|
Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Location in cell: plasma |
Molecular weight | Experimental: 10 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pINKWT |
Sequence | GO: MHC class I protein complex / InterPro: Beta-2-Microglobulin |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.3 mg/mL |
---|---|
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 |
-Electron microscopy
Microscope | FEI TECNAI F20 |
---|---|
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 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 29000 |
Sample stage | Specimen holder: side entry / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
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. |
---|---|
CTF correction | Details: Phase flipping |