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Structural transitions in RCNMV revealing potential mechanism of RNA release (EGTA map)
by single particle (icosahedral) reconstruction, at 9.0 A resolution
#1: Surface view with section colored by density value, Surface level: 11, Made by UCSF CHIMERA
#2: Surface view colored by radius, Surface level: 11, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 5372 |
|---|---|
| Authors | Sherman MB, Guenther RH, Tama F, Sit TL, Brooks CL, Mikhailov AM, Orlova EV, Baker TS, Lommel SA |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 11, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 11, 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. Virol., Vol. 80, Issue 21, Page 10395-406, Year 2006 |
|---|---|
| Title | Removal of divalent cations induces structural transitions in red clover necrotic mosaic virus, revealing a potential mechanism for RNA release. |
| Authors | Michael B Sherman, Richard H Guenther, Florence Tama, Tim L Sit, Charles L Brooks, Albert M Mikhailov, Elena V Orlova, Timothy S Baker, Steven A Lommel Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA. |
| Keywords |  Amino Acid Sequence, Calcium (metabolism, 7440-70-2), Capsid (metabolism), Capsid Proteins (genetics), Cations, Divalent (metabolism), Cryoelectron Microscopy, Image Processing, Computer-Assisted, Magnesium (metabolism, 7439-95-4), Models, Molecular, Molecular Sequence Data, Multiprotein Complexes, RNA, Viral (genetics), Sequence Homology, Amino Acid, Species Specificity, Static Electricity, Tombusviridae (genetics) |
| Links | DOI: 10.1128/JVI.01137-06, PubMed: 16920821, PMC: PMC1641784 |
 Map | |||||||||||||||||||||||||
| File |  EMD-5372.map ( map file in CCP4 format, 67110 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 = 512 A , B = 512 A , C = 512 A , alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 2 A , Y = 2 A , Z = 2 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | this is EM map of native RCNMV with EGTA | ||||||||||||||||||||||||
 Supplement |
 Sample | |
| Name | RCNMV |
|---|---|
| Number of Components | 1 |
| Theoretical Mass | 7 MDa |
| Details | monodisperse sample |
| Component #1: virus - RCNMV | |
| Scientific name | Red clover necrotic mosaic virus |
| Common Name | RCNMV |
| Theoretical Mass | 7 MDa |
| Experimental Mass | 7 MDa |
| Scientific Name of Species | Red clover necrotic mosaic virus (NCBI Taxonomy: 12267) |
| Common Name of Species | RCNMV |
| Empty | No |
| Enveloped | No |
| Isolate | SPECIES |
| Class | VIRION |
| Natural Source | Host Species: Dianthus (NCBI Taxonomy: 3569) Host Category: PLANTAE(HIGHER PLANTS) |
| Shell | Diameter: 366 A T Number: 3 |
 Experiment | |
| Sample Preparation | |
| Specimen Conc | 1 mg/ml |
|---|---|
| Specimen Support Details | 200 mesh Quantifoil |
| Specimen State | particle |
| Buffer | Details: 10 mM Tris-HCl pH: 6.5 |
| Vitrification | |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: cryo-plunger |
| Instrument | HOMEMADE PLUNGER |
| Temperature | 90 Kelvin |
| Imaging | |
| Microscope | FEI/PHILIPS CM300FEG/T |
| Date | 15-OCT-2003 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 300 kV |
| Electron Dose | 20 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 47000 X, Calibrated: 49523 X |
| Astigmatism | manual |
| Nominal Cs | 2.0 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 800 nm - 2800 nm |
| Specimen Holder | |
| Holder | GATAN 626 ( GATAN LIQUID NITROGEN ) |
| Tilt Angle | 0 degrees - 0 degrees |
| Temperature | 95 Kelvin ( 95 Kelvin - 123 Kelvin ) |
| Camera | |
| Detector | Kodak SO163 film |
| Image Acquisition | |
| Od Range | 1.5 |
| Scanner | ZEISS SCAI |
| Number of Digital Images | 1650 |
| Sampling Size | 7 microns |
| Quant Bit Number | 16 |
 Processing | |
| Method | single particle (icosahedral) reconstruction |
|---|---|
| 3 D reconstruction | |
| Algorithm | PFT |
| Software | PFT |
| CTF Correction | micrograph |
| Resolution By Author | 9.0 |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| Number of Projections | 4000 |
| Applied Symmetry | I (icosahedral) |
| Atomic Model Fitting | |
| Model #0 | |
| Details | Protocol: NNM |
| Software | SITUS |
| Refinement Space | REAL |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-5372.xml (8 KB) | ||
|---|---|---|---|
| Map data | emd_5372.map.gz (16.4 MB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5372 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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