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Open data
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Basic information
Entry | Database: PDB / ID: 3j7l | ||||||
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Title | Full virus map of brome mosaic virus | ||||||
![]() | Capsid protein | ||||||
![]() | VIRUS / capsid protein / BMV / beta barrel | ||||||
Function / homology | ![]() T=3 icosahedral viral capsid / host cell endoplasmic reticulum / viral nucleocapsid / ribonucleoprotein complex / structural molecule activity / RNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
![]() | Wang, Z. / Hryc, C. / Bammes, B. / Afonine, P.V. / Jakana, J. / Chen, D.H. / Liu, X. / Baker, M.L. / Kao, C. / Ludtke, S.J. ...Wang, Z. / Hryc, C. / Bammes, B. / Afonine, P.V. / Jakana, J. / Chen, D.H. / Liu, X. / Baker, M.L. / Kao, C. / Ludtke, S.J. / Schmid, M.F. / Adams, P.D. / Chiu, W. | ||||||
![]() | ![]() Title: An atomic model of brome mosaic virus using direct electron detection and real-space optimization. Authors: Zhao Wang / Corey F Hryc / Benjamin Bammes / Pavel V Afonine / Joanita Jakana / Dong-Hua Chen / Xiangan Liu / Matthew L Baker / Cheng Kao / Steven J Ludtke / Michael F Schmid / Paul D Adams / Wah Chiu / ![]() Abstract: Advances in electron cryo-microscopy have enabled structure determination of macromolecules at near-atomic resolution. However, structure determination, even using de novo methods, remains ...Advances in electron cryo-microscopy have enabled structure determination of macromolecules at near-atomic resolution. However, structure determination, even using de novo methods, remains susceptible to model bias and overfitting. Here we describe a complete workflow for data acquisition, image processing, all-atom modelling and validation of brome mosaic virus, an RNA virus. Data were collected with a direct electron detector in integrating mode and an exposure beyond the traditional radiation damage limit. The final density map has a resolution of 3.8 Å as assessed by two independent data sets and maps. We used the map to derive an all-atom model with a newly implemented real-space optimization protocol. The validity of the model was verified by its match with the density map and a previous model from X-ray crystallography, as well as the internal consistency of models from independent maps. This study demonstrates a practical approach to obtain a rigorously validated atomic resolution electron cryo-microscopy structure. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.4 KB | Display | ![]() |
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PDB format | ![]() | 79.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6000MC ![]() 3j7mC ![]() 3j7nC M: map data used to model this data C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 1.7 TB Data #1: Brome Mosaic Virus micrographs - non gain corrected [micrographs - multiframe] Data #2: Brome Mosaic Virus micrographs - gain corrected [micrographs - multiframe]) ![]() Data size: 23.1 Data #1: Brome Mosaic Virus boxed particles [picked particles - single frame - processed]) |
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Links
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Assembly
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3 | ![]()
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
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Components
#1: Protein | Mass: 20411.525 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Brome mosaic virus / Type: VIRUS |
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Details of virus | Empty: NO / Enveloped: NO / Host category: PLANTAE(HIGHER PLANTS) / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: Triticum aestivum |
Buffer solution | pH: 5.2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K / Details: Plunged into liquid ethane (FEI VITROBOT MARK IV). |
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Electron microscopy imaging
Microscopy | Model: JEOL 3200FSC / Date: Jan 10, 2013 |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Camera length: 0 mm |
Specimen holder | Specimen holder model: JEOL 3200FSC CRYOHOLDER |
Image recording | Film or detector model: DIRECT ELECTRON DE-12 (4k x 3k) |
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Processing
EM software |
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Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Method: Single Particle / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30000 / Nominal pixel size: 0.93 Å / Actual pixel size: 0.99 Å / Details: (Single particle--Applied symmetry: I) / Symmetry type: POINT | ||||||||||||
Refinement step | Cycle: LAST
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