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- EMDB-9281: CryoEM structure of chimeric Eastern Equine Encephalitis Virus: G... -
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Open data
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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 | |||||||||||||||
![]() | EEEV map low pass-filtered to 4.8A to visualize features of capsid N-terminal domain | |||||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() | |||||||||||||||
Method | ![]() ![]() | |||||||||||||||
![]() | Hasan SS / Sun C | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 524.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.3 KB 16.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 23.7 KB | Display | ![]() |
Images | ![]() | 269 KB | ||
Filedesc metadata | ![]() | 5.7 KB | ||
Others | ![]() ![]() | 238.7 MB 238.7 MB | ||
Archive directory | ![]() ![]() | 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 ( 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 | EEEV map low pass-filtered to 4.8A to visualize features of capsid N-terminal domain | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 |
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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: ![]() ![]() ![]() |
-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: ![]() ![]() ![]() |
Molecular weight | Theoretical: 28.861496 KDa |
Recombinant expression | Organism: ![]() ![]() |
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 | ![]() |
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Aggregation state | particle |
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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 |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 31.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | ![]() PDB-6mx7: |