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CryoEM reconstruction of the Marburg virus nucleocapsid.
by helical reconstruction, at 25 A resolution
#1: Surface view with section colored by density value, Surface level: 0.00124, Made by UCSF CHIMERA
#2: Surface view colored by cylindrical radius, Surface level: 0.00124, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1986 |
|---|---|
| Authors | Bharat TAM, Riches JD, Kolesnikova L, Welsch S, Kraehling V, Davey N, Parsy ML, Becker S, Briggs JAG |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 0.00124, Made by UCSF CHIMERA #2: Surface view colored by cylindrical radius, Surface level: 0.00124, 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 | PLoS Biol., Vol. 9, Issue 11, Page e1001196, Year 2011 |
|---|---|
| Title | Cryo-electron tomography of Marburg virus particles and their morphogenesis within infected cells. |
| Authors | Tanmay A M Bharat, James D Riches, Larissa Kolesnikova, Sonja Welsch, Verena Krähling, Norman Davey, Marie-Laure Parsy, Stephan Becker, John A G Briggs Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany. |
| Keywords |  Cell Line, Cryoelectron Microscopy, Electron Microscope Tomography, HEK293 Cells, Humans, Marburgvirus (chemistry), Nucleocapsid (metabolism), Nucleoproteins (metabolism), RNA, Viral, Rabies virus (physiology), VP24 protein, Marburg virus, VP35 protein, filovirus, Viral Proteins (chemistry), Viral Regulatory and Accessory Proteins (chemistry), Virus Assembly, Virus Release |
| Links | DOI: 10.1371/journal.pbio.1001196, PubMed: 22110401, PMC: PMC3217011 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1986.map ( map file in CCP4 format, 8102 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 | ||||||||||||||||||||||||
| Map Geometry |
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| Unit Cell | A = 600 A , B = 600 A , C = 360 A , alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 4 A , Y = 4 A , Z = 4 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | This is a map of the Marburg virus nucleocapsid within virions. | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | Marburg virus nucleocapsid |
|---|---|
| Number of Components | 1 |
| Component #1: virus - Marburg virus | |
| Scientific name | Marburg marburgvirus |
| Common Name | Marburg virus |
| Scientific Name of Species | Marburg marburgvirus (NCBI Taxonomy: 11269) |
| Common Name of Species | Marburg virus |
| Empty | No |
| Enveloped | Yes |
| Isolate | STRAIN |
| Class | VIRION |
| Natural Source | Host Species: Homo sapiens (NCBI Taxonomy: 9606) Host Category: VERTEBRATES |
 Experiment | |
| Sample Preparation | |
| Helical Parameters | Delta Z: 5.0 A Delta Phi: 24.3 degrees Hand: LEFT HANDED |
|---|---|
| Specimen State | filament |
| Buffer | Details: PBS buffer with 4% PFA. |
| Vitrification | |
| Method | Plunge freezing |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: Plunge freezer |
| Instrument | HOMEMADE PLUNGER |
| Imaging | |
| Microscope | FEI/PHILIPS CM120T |
| Electron Gun | |
| Electron Source | LAB6 |
| Accelerating Voltage | 120 kV |
| Electron Dose | 10 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 37000 X, |
| Nominal Cs | 6.3 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 0.6 nm - 4.0 nm |
| Specimen Holder | |
| Holder | Gatan 626 ( GATAN LIQUID NITROGEN ) |
| Tilt Angle | 0 degrees - 0 degrees |
| Camera | |
| Detector | Kodak SO163 film |
| Image Acquisition | |
| Scanner | ZEISS SCAI |
| Sampling Size | 14 microns |
 Processing | |
| Method | helical reconstruction |
|---|---|
| 3 D reconstruction | |
| Algorithm | real-space helical |
| Software | Spider, Bsoft |
| CTF Correction | Phase flip |
| Resolution By Author | 25 |
| Resolution Method | FSC at 0.5 cut-off |
| Atomic Model Fitting | |
| Model #0 | |
| Details | Protocol: Rigid body. 4 monomers from the VSV Nucleoprotein structure were fitted in as a single rigid body without any corrections. |
| Software | Chimera |
| Refinement Protocol | rigid body |
| Refinement Space | REAL |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-1986.xml (7.1 KB) | ||
|---|---|---|---|
| Map data | emd_1986.map.gz (7.3 MB) | ||
| Images |  emd-1986.jpg (37.2 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1986 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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