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Cryo-EM of Rift Valley fever virus
by single particle (icosahedral) reconstruction, at 27 A resolution
#1: Surface view with section colored by density value, Surface level: 7.3, Made by UCSF CHIMERA
#2: Surface view colored by radius, Surface level: 7.3, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 5124 |
|---|---|
| Title | Cryo-EM of Rift Valley fever virus |
| Map | this is RVFV map in 2-fold orientation |
| Sample | Rift Valley fever virus, RVFV vaccine strain MP-12 |
| Keywords |  cryo-electron microscopy, single particle averaging, Rift valley fever, bunyaviridae, inter-capsomer contacts |
| Authors | Sherman MB, Freiberg AN, Holbrook AM, Watowich SJ |
| Date | Deposition: 2009-07-20, Header release: 2009-07-24, Map release: 2009-07-24, Last update: 2011-07-08 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 7.3, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 7.3, Made by UCSF CHIMERA |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - Primary | |
| Article | Virology, Vol. 387, Issue 1, Page 11-5, Year 2009 |
|---|---|
| Title | Single-particle cryo-electron microscopy of Rift Valley fever virus. |
| Authors | Michael B Sherman, Alexander N Freiberg, Michael R Holbrook, Stanley J Watowich Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-0647, USA. |
| Keywords | Cryoelectron Microscopy (methods), Glycoproteins (metabolism), Image Processing, Computer-Assisted, Membrane Lipids (metabolism), Rift Valley fever virus (ultrastructure), Viral Envelope Proteins (metabolism), viral envelope lipids |
| Links | DOI: 10.1016/j.virol.2009.02.038, PubMed: 19304307, PMC: PMC2673237 |
| Citation - #1 | |
| Article | J.VIROL., Vol. 82, Page 10341-10348, Year 2008 |
| Title | Three-dimensional organization of Rift Valley fever virus revealed by cryoelectron tomography |
| Authors | Freiberg AN, Sherman MB, Morais MC, Holbrook MR, Watowich SJ |
 Map | |||||||||||||||||||||||||
| File |  EMD-5124.map ( map file in CCP4 format, 366937 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= B= C: 1353 A Alpha=beta=gamma: 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X= Y= Z: 3 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | this is RVFV map in 2-fold orientation | ||||||||||||||||||||||||
 Supplement |
 Sample | |
| Name | Rift Valley fever virus, RVFV vaccine strain MP-12 |
|---|---|
| Number of Components | 8 |
| Oligomeric State | single virions |
| Details | monodisperse sample |
| Component #1: virus - RVFV | |
| Scientific name | Rift Valley fever virus |
| Common Name | RVFV |
| Details | 100 nm particles |
| Scientific Name of Species | Rift Valley fever virus |
| Common Name of Species | RVFV |
| NCBI taxonomy | 11588 |
| Empty | No |
| Enveloped | Yes |
| Isolate | STRAIN |
| Class | VIRION |
| Natural Source | NCBI taxonomy: 9606 Host Species: Homo sapiens Host Category: VERTEBRATES |
| Shell | Id: 1 , Diameter: 1000 A, T Number: 12 |
 Experiment | |
| Sample Preparation | |
| Specimen Conc | 0.1 mg/ml |
|---|---|
| Specimen Support Details | 200 mesh copper Qauntifoil grids |
| Specimen State | particle |
| Buffer | Details: 10 mM Tris-HCl, 100 mM NaCl, 1 mM EDTA pH: 7.2 |
| Vitrification | |
| Method | blot 2 sec before plunging |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: pneumatic plunger |
| Humidity | 80 |
| Instrument | HOMEMADE PLUNGER |
| Temperature | 95 Kelvin |
| Imaging | |
| Microscope | JEOL 2200FS |
| Date | 01-Nov-2007 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Electron Dose | 20 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 40000, Calibrated: 40200 |
| Astigmatism | objective lens astigmatism was corrected at 100,000 times magnification |
| Nominal Cs | 2 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 700 nm - 3700 nm |
| Energy Filter | Energy Filter: omega , Energy Window: 0-20 eV |
| Specimen Holder | |
| Holder | Eucentric |
| Model | GATAN LIQUID NITROGEN |
| Tilt Angle | 0 degrees - 0 degrees |
| Temperature | 99 K ( 99 - 99 K) |
| Camera | |
| Detector | Ultrascan 895 |
| Image Acquisition | |
| Number of Digital Images | 93 |
| Sampling Size | 14 |
| Quant Bit Number | 16 |
 Processing | |
| Method | single particle (icosahedral) reconstruction |
|---|---|
| 3D reconstruction | |
| Algorithm | PFT |
| Software | PFT |
| CTF Correction | Each particle |
| Details | Final map calculated from 108 particles |
| Resolution By Author | 27 A |
| Resolution Method | FSC |
| Single Particle | |
| Number of Projections | 108 |
| Number of Class Averages | 1 |
| Applied Symmetry | I (icosahedral) |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-5124.xml (8.5 KB) | ||
|---|---|---|---|
| Map data | emd_5124.map.gz (144.3 MB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5124 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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