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Mutually-induced conformational switching of RNA and coat protein underpins efficient assembly of a viral capsid.
by single particle (icosahedral) reconstruction, at 17.5 A resolution
#1: Surface view with section colored by density value, Surface level: 1, Made by UCSF CHIMERA
#2: Surface view colored by radius, Surface level: 1, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1880 |
|---|---|
| Authors | Rolfsson O, Toropova K, Ranson NA, Stockley PG |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 1, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 1, 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. 401, Issue 2, Page 309-22, Year 2010 |
|---|---|
| Title | Mutually-induced conformational switching of RNA and coat protein underpins efficient assembly of a viral capsid. |
| Authors | Ottar Rolfsson, Katerina Toropova, Neil A Ranson, Peter G Stockley Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK. |
| Keywords |  Base Sequence, Capsid (chemistry), Capsid Proteins (chemistry), Cryoelectron Microscopy, DNA Primers (genetics), Imaging, Three-Dimensional, Levivirus (chemistry), Models, Molecular, Nucleic Acid Conformation, Protein Conformation, RNA, Viral (chemistry), Recombinant Proteins (chemistry), Virus Assembly (physiology) |
| Links | PubMed: 20684044 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1880.map ( map file in CCP4 format, 32002 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 = 374 A , B = 374 A , C = 374 A , alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 1.87 A , Y = 1.87 A , Z = 1.87 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | This is a surface rendered view of a Bacteriophage MS2 virus-like particle composed of purified coat protein and a 5' genomic RNA fragment (5'RNA). | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | Bacteriophage MS2 virus-like particles assembled in vitro from purified MS2 coat protein and 5' genomic RNA fragments (nts 1-2469). |
|---|---|
| Number of Components | 2 |
| Oligomeric State | One capsid to one RNA |
| Component #1: virus - MS2 | |
| Scientific name | Enterobacterio phage MS2 |
| Common Name | MS2 |
| Scientific Name of Species | Enterobacterio phage MS2 (NCBI Taxonomy: 12022) |
| Common Name of Species | MS2 |
| Enveloped | No |
| Empty | No |
| Class | VIRUS-LIKE PARTICLE |
| Isolate | STRAIN |
| Natural Source | Host Category: BACTERIA(EUBACTERIA) Host Species: Escherichia coli (NCBI Taxonomy: 562) |
| Shell | T Number: 3 Diameter: 280 A |
| Component #2: nucleic-acid - Single stranded MS2 RNA | |
| Scientific name | Single stranded MS2 RNA |
| Details | nucleotides 1-2469 was made by in vitro transcription from a cDNA template of the MS2 genome. |
| Scientific Name of Species | Enterobacteria phage MS2 (NCBI Taxonomy: 329852) |
| Common Name of Species | MS2 |
| Class | RNA |
| Structure | SINGLE STRANDED |
| Synthetic | No |
 Experiment | |
| Sample Preparation | |
| Specimen Support Details | Quantifoil R2/1 200 mesh holly carbon grid |
|---|---|
| Specimen State | particle |
| Buffer | Details: 50mM Tris-acetate, 1mM magnesium acetate, 40mM ammonium acetate pH: 7.6 |
| Vitrification | |
| Method | 1.6s blot |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: Double-sided custom pneumatic blotter |
| Instrument | HOMEMADE PLUNGER |
| Imaging | |
| Microscope | FEI TECNAI F20 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Electron Dose | 18 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 50000 X, Calibrated: 52750 X |
| Nominal Cs | 2 mm |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder | |
| Holder | Side entry ( GATAN LIQUID NITROGEN ) |
| Camera | |
| Image Acquisition | |
| Scanner | OTHER |
| Sampling Size | 9.88 microns |
| Quant Bit Number | 16 |
 Processing | |
| Method | single particle (icosahedral) reconstruction |
|---|---|
| 3 D reconstruction | |
| Algorithm | Projection matching |
| Software | Spider |
| CTF Correction | Phase flip each particle |
| Resolution By Author | 17.5 |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| Number of Projections | 1538 |
| Number of Class Averages | 53 |
| Applied Symmetry | I (icosahedral) |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-1880.xml (7.8 KB) | ||
|---|---|---|---|
| Map data | emd_1880.map.gz (24.5 MB) | ||
| Images |  emd1880.jpg (140.3 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1880 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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