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Yorodumi- EMDB-5276: 4.4 Angstrom Cryo-EM Structure of an Enveloped Alphavirus Venezue... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5276 | |||||||||
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Title | 4.4 Angstrom Cryo-EM Structure of an Enveloped Alphavirus Venezuelan Equine Encephalitis Virus | |||||||||
Map data | This is a non-icosahedrally averaged map of Venezuelan Equine Encephalitis Virus from the 4 unique sets of E1-E2-E3-CP molecules within one asymmetric unit of the original 3D density map. | |||||||||
Sample |
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Keywords | alphavirus / bioweapon / cryoEM / modeling / VEEV | |||||||||
Function / homology | Function and homology information togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host gene expression / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host gene expression / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / RNA binding / membrane Similarity search - Function | |||||||||
Biological species | Venezuelan equine encephalitis virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.8 Å | |||||||||
Authors | Zhang R / Hryc CF / Cong Y / Liu X / Jakana J / Gorchakov R / Baker ML / Weaver SC / Chiu W | |||||||||
Citation | Journal: EMBO J / Year: 2011 Title: 4.4 Å cryo-EM structure of an enveloped alphavirus Venezuelan equine encephalitis virus. Authors: Rui Zhang / Corey F Hryc / Yao Cong / Xiangan Liu / Joanita Jakana / Rodion Gorchakov / Matthew L Baker / Scott C Weaver / Wah Chiu / Abstract: Venezuelan equine encephalitis virus (VEEV), a member of the membrane-containing Alphavirus genus, is a human and equine pathogen, and has been developed as a biological weapon. Using electron cryo- ...Venezuelan equine encephalitis virus (VEEV), a member of the membrane-containing Alphavirus genus, is a human and equine pathogen, and has been developed as a biological weapon. Using electron cryo-microscopy (cryo-EM), we determined the structure of an attenuated vaccine strain, TC-83, of VEEV to 4.4 Å resolution. Our density map clearly resolves regions (including E1, E2 transmembrane helices and cytoplasmic tails) that were missing in the crystal structures of domains of alphavirus subunits. These new features are implicated in the fusion, assembly and budding processes of alphaviruses. Furthermore, our map reveals the unexpected E3 protein, which is cleaved and generally thought to be absent in the mature VEEV. Our structural results suggest a mechanism for the initial stage of nucleocapsid core formation, and shed light on the virulence attenuation, host recognition and neutralizing activities of VEEV and other alphavirus pathogens. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5276.map.gz | 1.8 MB | EMDB map data format | |
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Header (meta data) | emd-5276-v30.xml emd-5276.xml | 11.7 KB 11.7 KB | Display Display | EMDB header |
Images | emd_5276_1.png | 107.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5276 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5276 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_5276.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a non-icosahedrally averaged map of Venezuelan Equine Encephalitis Virus from the 4 unique sets of E1-E2-E3-CP molecules within one asymmetric unit of the original 3D density map. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Venezuelan Equine Encephalitis Virus TC-83 Strain
Entire | Name: Venezuelan Equine Encephalitis Virus TC-83 Strain |
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Components |
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-Supramolecule #1000: Venezuelan Equine Encephalitis Virus TC-83 Strain
Supramolecule | Name: Venezuelan Equine Encephalitis Virus TC-83 Strain / type: sample / ID: 1000 Details: The viruses were purified from infected Baby hamster kidney (BHK) cells Oligomeric state: E1-E2-E3-CP complex / Number unique components: 4 |
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Molecular weight | Theoretical: 52 MDa |
-Supramolecule #1: Venezuelan equine encephalitis virus
Supramolecule | Name: Venezuelan equine encephalitis virus / type: virus / ID: 1 / Name.synonym: VEEV / NCBI-ID: 11036 / Sci species name: Venezuelan equine encephalitis virus / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: VEEV |
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Host (natural) | Organism: Equus caballus (horse) / synonym: VERTEBRATES |
Molecular weight | Theoretical: 52 MDa |
Virus shell | Shell ID: 1 / Diameter: 700 Å / T number (triangulation number): 4 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Grid | Details: 400 mesh Quantifoil R 1.2/1.3 copper grids |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 100 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: 2 blots, each blot 2 seconds before plunging |
-Electron microscopy
Microscope | JEOL 3200FSC |
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Temperature | Average: 96 K |
Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification |
Specialist optics | Energy filter - Name: Omega Filter |
Date | Apr 9, 2008 |
Image recording | Category: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Number real images: 4000 / Average electron dose: 18 e/Å2 / Camera length: 200 / Details: 4kx4k CCD Image |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.3 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 100000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: JEOL 3200FSC CRYOHOLDER |
-Image processing
Details | The virus particles were automatically boxed out using ethan, among which around 10,000 particles contained continuous carbon film. |
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CTF correction | Details: Each frame |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN Details: This is a non-icosahedrally averaged map of Venezuelan Equine Encephalitis Virus from the 4 unique sets of E1-E2-E3-CP molecules within one asymmetric unit of the original 3D density map Number images used: 37000 |
Final two d classification | Number classes: 1000 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Details | Protocol: Rigid Body |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-3j0c: PDB-3j0g: |