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Globular tetramers of beta-2-microglobulin assemble into elaborate amyloid fibrils
by helical reconstruction, at 25 A resolution
#1: Surface view with section colored by density value, Surface level: 0.5, Made by UCSF CHIMERA
#2: Surface view colored by cylindrical radius, Surface level: 0.5, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1614 |
|---|---|
| Authors | White HE, Hodgkinson JL, Jahn TR, Cohen-Krausz S, Gosal WS, Muller S, Orlova EV, Radford SE, Saibil HR |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 0.5, Made by UCSF CHIMERA #2: Surface view colored by cylindrical radius, Surface level: 0.5, Made by UCSF CHIMERA |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - Primary | |
| Article | J. Mol. Biol., Vol. 389, Issue 1, Page 48-57, 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 Department of Crystallography and Institute of Structural and Molecular Biology, Birkbeck College, London, UK. |
| Keywords |  Amyloid (chemistry), Models, Molecular, Protein Structure, Quaternary, Protein Structure, Secondary, Protein Subunits (chemistry), beta 2-Microglobulin (chemistry) |
| Links | PII: S0022-2836(09)00392-1, DOI: 10.1016/j.jmb.2009.03.066, PubMed: 19345691, PMC: PMC2726924 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1614.map ( map file in CCP4 format, 2050 KB ) | ||||||||||||||||||||||||
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| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
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| Data Type | Image stored as Reals | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
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| Unit Cell | A = 280 A , B = 280 A , C = 280 A , alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 3.5 A , Y = 3.5 A , Z = 3.5 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | Surface view of an B-type map from beta-2-microglobulin | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | beta-2-microglobulin |
|---|---|
| Number of Components | 1 |
| Experimental Mass | 0.01 MDa |
| Component #1: protein - beta-2-microglobulin | |
| Scientific name | beta-2-microglobulin |
| Experimental Mass | 0.01 MDa |
| Oligomeric Details | monomer |
| Scientific Name of Species | Homo sapiens (NCBI Taxonomy: 9606) |
| Common Name of Species | Human |
| Recombinant expression | Yes |
| Natural Source | Cell Location: plasma |
| Engineered Source | Vector: pINKWT Exp System: Escherichia coli (NCBI Taxonomy: 562) |
| Links | InterPro: IPR:015707, Gene Ontology: GO:0042612 |
 Experiment | |
| Sample Preparation | |
| Helical Parameters | Delta Z: 52.5 A Delta Phi: 7.01 degrees Hand: LEFT HANDED |
|---|---|
| Specimen Conc | 0.3 mg/ml |
| Specimen Support Details | holey carbon grids |
| Specimen State | filament |
| Buffer | pH: 2.5 Details: 25 mM sodium phosphate, 25 mM sodium acetate |
| Vitrification | |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: manual plunger |
| Instrument | HOMEMADE PLUNGER |
| Imaging | |
| Microscope | FEI TECNAI F20 |
| Details | Low dose |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 29000 X, |
| Nominal Cs | 2 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 1000 nm - 2600 nm |
| Specimen Holder | |
| Holder | side entry ( GATAN LIQUID NITROGEN ) |
| Temperature | ( 100 Kelvin - ) |
| Camera | |
| Detector | Kodak SO163 film |
| Image Acquisition | |
| Scanner | ZEISS SCAI |
| Number of Digital Images | 85 |
| Sampling Size | 7 microns |
| Quant Bit Number | 8 |
 Processing | |
| Method | helical reconstruction |
|---|---|
| 3 D reconstruction | |
| Algorithm | Back projection using helical parameters |
| Software | SPIDER |
| CTF Correction | Phase flipping |
| Details | Maps were calculated for each class as each class had a different pitch. |
| Resolution By Author | 25 |
| Resolution Method | FSC at 0.5 cut-off |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-1614.xml (7.3 KB) | ||
|---|---|---|---|
| Map data | emd_1614.map.gz (1.7 MB) | ||
| Images | 1614.tif (737.6 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1614 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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