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Yorodumi- EMDB-5275: 4.4 Angstrom Cryo-EM Structure of an Enveloped Alphavirus Venezue... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5275 | |||||||||
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Title | 4.4 Angstrom Cryo-EM Structure of an Enveloped Alphavirus Venezuelan Equine Encephalitis Virus | |||||||||
Map data | This is a portion of the original 3D density map (size 800x800x800 pixels) of Venezuelan Equine Encephalitis Virus TC-83 strain. | |||||||||
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_5275.map.gz | 59.2 MB | EMDB map data format | |
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Header (meta data) | emd-5275-v30.xml emd-5275.xml | 11.3 KB 11.3 KB | Display Display | EMDB header |
Images | emd_5275_1.png | 477 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5275 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5275 | HTTPS FTP |
-Validation report
Summary document | emd_5275_validation.pdf.gz | 497.9 KB | Display | EMDB validaton report |
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Full document | emd_5275_full_validation.pdf.gz | 497.4 KB | Display | |
Data in XML | emd_5275_validation.xml.gz | 6.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5275 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5275 | HTTPS FTP |
-Related structure data
Related structure data | 3j0cMC 3j0gMC 5276C M: atomic model generated by this map C: citing same article (ref.) |
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Similar 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_5275.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a portion of the original 3D density map (size 800x800x800 pixels) of Venezuelan Equine Encephalitis Virus TC-83 strain. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 Details: The VEEV virus has 240 copies of E1, E2, and CP arranged in icosahedral symmetry 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) / Average electron dose: 18 e/Å2 / Camera length: 200 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 3.2 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
CTF correction | Details: Each frame |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / 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: |