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Yorodumi- EMDB-9281: CryoEM structure of chimeric Eastern Equine Encephalitis Virus: G... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9281 | |||||||||||||||
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Title | CryoEM structure of chimeric Eastern Equine Encephalitis Virus: Genome-Binding Capsid N-terminal Domain | |||||||||||||||
Map data | EEEV map low pass-filtered to 4.8A to visualize features of capsid N-terminal domain | |||||||||||||||
Sample |
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Keywords | Alphavirus / EEEV / Eastern Equine Encephalitis Virus / Sindbis / VIRUS | |||||||||||||||
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 / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host gene expression / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / 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 | Eastern equine encephalitis virus | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.8 Å | |||||||||||||||
Authors | Hasan SS / Sun C | |||||||||||||||
Funding support | United States, United Kingdom, 4 items
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Citation | Journal: Cell Rep / Year: 2018 Title: Cryo-EM Structures of Eastern Equine Encephalitis Virus Reveal Mechanisms of Virus Disassembly and Antibody Neutralization. Authors: S Saif Hasan / Chengqun Sun / Arthur S Kim / Yasunori Watanabe / Chun-Liang Chen / Thomas Klose / Geeta Buda / Max Crispin / Michael S Diamond / William B Klimstra / Michael G Rossmann / Abstract: Alphaviruses are enveloped pathogens that cause arthritis and encephalitis. Here, we report a 4.4-Å cryoelectron microscopy (cryo-EM) structure of eastern equine encephalitis virus (EEEV), an ...Alphaviruses are enveloped pathogens that cause arthritis and encephalitis. Here, we report a 4.4-Å cryoelectron microscopy (cryo-EM) structure of eastern equine encephalitis virus (EEEV), an alphavirus that causes fatal encephalitis in humans. Our analysis provides insights into viral entry into host cells. The envelope protein E2 showed a binding site for the cellular attachment factor heparan sulfate. The presence of a cryptic E2 glycan suggests how EEEV escapes surveillance by lectin-expressing myeloid lineage cells, which are sentinels of the immune system. A mechanism for nucleocapsid core release and disassembly upon viral entry was inferred based on pH changes and capsid dissociation from envelope proteins. The EEEV capsid structure showed a viral RNA genome binding site adjacent to a ribosome binding site for viral genome translation following genome release. Using five Fab-EEEV complexes derived from neutralizing antibodies, our investigation provides insights into EEEV host cell interactions and protective epitopes relevant to vaccine design. | |||||||||||||||
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_9281.map.gz | 524.5 MB | EMDB map data format | |
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Header (meta data) | emd-9281-v30.xml emd-9281.xml | 16.3 KB 16.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9281_fsc.xml | 23.7 KB | Display | FSC data file |
Images | emd_9281.png | 269 KB | ||
Filedesc metadata | emd-9281.cif.gz | 5.7 KB | ||
Others | emd_9281_half_map_1.map.gz emd_9281_half_map_2.map.gz | 238.7 MB 238.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9281 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9281 | HTTPS FTP |
-Validation report
Summary document | emd_9281_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_9281_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_9281_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | emd_9281_validation.cif.gz | 38.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9281 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9281 | HTTPS FTP |
-Related structure data
Related structure data | 6mx7MC 9249C 9274C 9275C 9278C 9279C 9280C 6muiC 6mw9C 6mwcC 6mwvC 6mwxC 6mx4C C: citing same article (ref.) M: atomic model generated by this map |
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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_9281.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | EEEV map low pass-filtered to 4.8A to visualize features of capsid N-terminal domain | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.58 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: EEEV half map
File | emd_9281_half_map_1.map | ||||||||||||
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Annotation | EEEV half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: EEEV half map
File | emd_9281_half_map_2.map | ||||||||||||
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Annotation | EEEV half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Eastern equine encephalitis virus capsid
Entire | Name: Eastern equine encephalitis virus capsid |
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Components |
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-Supramolecule #1: Eastern equine encephalitis virus capsid
Supramolecule | Name: Eastern equine encephalitis virus capsid / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Purified from infected BHK-15 cells |
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Source (natural) | Organism: Eastern equine encephalitis virus |
-Macromolecule #1: Capsid
Macromolecule | Name: Capsid / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Eastern equine encephalitis virus |
Molecular weight | Theoretical: 28.861496 KDa |
Recombinant expression | Organism: Mesocricetus auratus (golden hamster) |
Sequence | String: MFPYPTLNYP PMAPINPMAY RDPNPPRQVA PFRPPLAAQI EDLRRSIANL TLKQRAPNPP AGPPAKRKKP APKPKPAQAK KKRPPPPAK KQKRKPKPGK RQRMCMKLES DKTFPIMLNG QVNGYACVVG GRVFKPLHVE GRIDNEQLAA IKLKKASIYD L EYGDVPQC ...String: MFPYPTLNYP PMAPINPMAY RDPNPPRQVA PFRPPLAAQI EDLRRSIANL TLKQRAPNPP AGPPAKRKKP APKPKPAQAK KKRPPPPAK KQKRKPKPGK RQRMCMKLES DKTFPIMLNG QVNGYACVVG GRVFKPLHVE GRIDNEQLAA IKLKKASIYD L EYGDVPQC MKSDTLQYTS DKPPGFYNWH HGAVQYENNR FTVPRGVGGK GDSGRPILDN KGRVVAIVLG GVNEGSRTAL SV VTWNQKG VTVKDTPEGS EPW UniProtKB: Structural polyprotein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.5 |
Grid | Details: unspecified |
Vitrification | Cryogen name: HELIUM / Chamber humidity: 80 % / Chamber temperature: 295 K / Instrument: GATAN CRYOPLUNGE 3 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 31.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-6mx7: |