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Yorodumi- PDB-5a33: Electron cryo-microscopy of Cowpea Mosaic Virus (CPMV) empty viru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a33 | ||||||
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Title | Electron cryo-microscopy of Cowpea Mosaic Virus (CPMV) empty virus like particle (eVLP) | ||||||
Components | (RNA2 POLYPROTEIN) x 2 | ||||||
Keywords | VIRUS / CPMV / EVLP / COMOVIRIDAE / PICORNAVIRALES. | ||||||
Function / homology | Function and homology information transport of virus in host, cell to cell / host cell plasmodesma / T=3 icosahedral viral capsid / symbiont-mediated suppression of host innate immune response / virus-mediated perturbation of host defense response / host cell nucleus / GTP binding / structural molecule activity / DNA binding / RNA binding Similarity search - Function | ||||||
Biological species | COWPEA MOSAIC VIRUS | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.04 Å | ||||||
Authors | Hesketh, E.L. / Meshcheriakova, Y. / Dent, K.C. / Saxena, P. / Thompson, R. / Cockburn, J.J. / Lomonossoff, G.P. / Ranson, N.A. | ||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Mechanisms of assembly and genome packaging in an RNA virus revealed by high-resolution cryo-EM. Authors: Emma L Hesketh / Yulia Meshcheriakova / Kyle C Dent / Pooja Saxena / Rebecca F Thompson / Joseph J Cockburn / George P Lomonossoff / Neil A Ranson / Abstract: Cowpea mosaic virus is a plant-infecting member of the Picornavirales and is of major interest in the development of biotechnology applications. Despite the availability of >100 crystal structures of ...Cowpea mosaic virus is a plant-infecting member of the Picornavirales and is of major interest in the development of biotechnology applications. Despite the availability of >100 crystal structures of Picornavirales capsids, relatively little is known about the mechanisms of capsid assembly and genome encapsidation. Here we have determined cryo-electron microscopy reconstructions for the wild-type virus and an empty virus-like particle, to 3.4 Å and 3.0 Å resolution, respectively, and built de novo atomic models of their capsids. These new structures reveal the C-terminal region of the small coat protein subunit, which is essential for virus assembly and which was missing from previously determined crystal structures, as well as residues that bind to the viral genome. These observations allow us to develop a new model for genome encapsidation and capsid assembly. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5a33.cif.gz | 122.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a33.ent.gz | 95.5 KB | Display | PDB format |
PDBx/mmJSON format | 5a33.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a33_validation.pdf.gz | 806.4 KB | Display | wwPDB validaton report |
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Full document | 5a33_full_validation.pdf.gz | 807.1 KB | Display | |
Data in XML | 5a33_validation.xml.gz | 29 KB | Display | |
Data in CIF | 5a33_validation.cif.gz | 42.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/5a33 ftp://data.pdbj.org/pub/pdb/validation_reports/a3/5a33 | HTTPS FTP |
-Related structure data
Related structure data | 3014MC 3013C 5a32C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given / Matrix: (1), |
-Components
#1: Protein | Mass: 23798.902 Da / Num. of mol.: 1 / Fragment: LARGE COAT PROTEIN Source method: isolated from a genetically manipulated source Details: EMPTY VIRUS LIKE PARTICLES (EVLPS) PRODUCED BY EXPRESSING A COAT PRECURSOR PROTEIN VP60 WHICH EXPRESSED BOTH LARGE AND SMALL PROTEINS AND THE 24K PROTEASE IN N. BENTHAMIANA Source: (gene. exp.) COWPEA MOSAIC VIRUS / Production host: NICOTIANA BENTHAMIANA (plant) / References: UniProt: P03599 |
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#2: Protein | Mass: 40858.434 Da / Num. of mol.: 1 / Fragment: SMALL COAT PROTEIN Source method: isolated from a genetically manipulated source Details: EMPTY VIRUS LIKE PARTICLES (EVLPS) PRODUCED BY EXPRESSING A COAT PRECURSOR PROTEIN VP60 WHICH EXPRESSED BOTH LARGE AND SMALL PROTEINS AND THE 24K PROTEASE IN N. BENTHAMIANA Source: (gene. exp.) COWPEA MOSAIC VIRUS / Production host: NICOTIANA BENTHAMIANA (plant) / References: UniProt: P03599 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: COWPEA MOSAIC VIRUS / Type: VIRUS |
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Specimen | Conc.: 4.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Nov 1, 2014 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 134615 X / Calibrated magnification: 134615 X / Nominal defocus max: 5000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm |
Image recording | Electron dose: 45 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
Image scans | Num. digital images: 1135 |
-Processing
EM software | Name: RELION / Version: 1.3 / Category: 3D reconstruction | ||||||||||||
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CTF correction | Details: CTFFIND3 PER MICROGRAPH | ||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Resolution: 3.04 Å / Num. of particles: 4998 / Nominal pixel size: 1.04 Å / Actual pixel size: 1.04 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3014. (DEPOSITION ID: 13384). Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL / Target criteria: R-factor / Details: REFINEMENT PROTOCOL--EM | ||||||||||||
Refinement | Highest resolution: 3.04 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3.04 Å
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