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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-8249 | |||||||||
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Title | Subtomogram-averaged map of a single rubella virus capsid unit | |||||||||
![]() | Subtomogram-averaged single capsid unit | |||||||||
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Function / homology | ![]() T=4 icosahedral viral capsid / host cell Golgi membrane / host cell mitochondrion / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / RNA binding ...T=4 icosahedral viral capsid / host cell Golgi membrane / host cell mitochondrion / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / RNA binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 35.0 Å | |||||||||
![]() | Mangala Prasad V / Klose T / Rossmann MG | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Assembly, maturation and three-dimensional helical structure of the teratogenic rubella virus. Authors: Vidya Mangala Prasad / Thomas Klose / Michael G Rossmann / ![]() Abstract: Viral infections during pregnancy are a significant cause of infant morbidity and mortality. Of these, rubella virus infection is a well-substantiated example that leads to miscarriages or severe ...Viral infections during pregnancy are a significant cause of infant morbidity and mortality. Of these, rubella virus infection is a well-substantiated example that leads to miscarriages or severe fetal defects. However, structural information about the rubella virus has been lacking due to the pleomorphic nature of the virions. Here we report a helical structure of rubella virions using cryo-electron tomography. Sub-tomogram averaging of the surface spikes established the relative positions of the viral glycoproteins, which differed from the earlier icosahedral models of the virus. Tomographic analyses of in vitro assembled nucleocapsids and virions provide a template for viral assembly. Comparisons of immature and mature virions show large rearrangements in the glycoproteins that may be essential for forming the infectious virions. These results present the first known example of a helical membrane-enveloped virus, while also providing a structural basis for its assembly and maturation pathway. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 14.4 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.8 KB 12.8 KB | Display Display | ![]() |
Images | ![]() | 56.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 323.2 KB | Display | ![]() |
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Full document | ![]() | 322.7 KB | Display | |
Data in XML | ![]() | 4.5 KB | Display | |
Data in CIF | ![]() | 5.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kheMC ![]() 8248C ![]() 8250C ![]() 8251C ![]() 5khcC ![]() 5khfC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Subtomogram-averaged single capsid unit | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Rubella virus strain M33
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Rubella virus strain M33
Supramolecule | Name: Rubella virus strain M33 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Molecular weight | Theoretical: 64 KDa |
-Macromolecule #1: capsid protein
Macromolecule | Name: capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 30.016332 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MEDLQKALEA QSRALRAELA AGASQSRRPR PPRQRDSSTS GDDSGRDSGG PRRRRGNRGR GQRRDWSRAP PPPEERQETR SQTPAPKPS RAPPQQPQPP RMQTGRGGSA PRPELGPPTN PFQAAVARGL RPPLHDPDTE APTEACVTSW LWSEGEGAVF Y RVDLHFTN ...String: MEDLQKALEA QSRALRAELA AGASQSRRPR PPRQRDSSTS GDDSGRDSGG PRRRRGNRGR GQRRDWSRAP PPPEERQETR SQTPAPKPS RAPPQQPQPP RMQTGRGGSA PRPELGPPTN PFQAAVARGL RPPLHDPDTE APTEACVTSW LWSEGEGAVF Y RVDLHFTN LGTPPLDEDG RWDPALMYNP CGPEPPAHVV RAYNQPAGDV RGVWGKGERT YAEQDFRVGG TRWHRLLRMP VR GLDGDSA PLPPHTTERI ETRSARHPWR IR |
-Macromolecule #2: water
Macromolecule | Name: water / type: ligand / ID: 2 / Number of copies: 35 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL | |||||||||
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Buffer | pH: 7.2 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON | |||||||||
Vitrification | Cryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3 |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus min: 0.5 µm / Nominal magnification: 11000 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 35.0 Å / Resolution method: OTHER / Software - Name: PEET (ver. 10.1) / Number subtomograms used: 18 |
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Extraction | Number tomograms: 15 / Number images used: 20 / Reference model: none / Method: manual picking / Software - Name: IMOD/PEET (ver. 4.8.40/10.1) |
CTF correction | Software - Name: ![]() |
Final angle assignment | Type: OTHER |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: sumf |
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Output model | ![]() PDB-5khe: |