+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9280 | |||||||||||||||
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Title | CryoEM structure of chimeric Eastern Equine Encephalitis Virus | |||||||||||||||
Map data | EEEV 4.4 Angstrom Full Map | |||||||||||||||
Sample |
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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 / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Eastern equine encephalitis virus | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||||||||
Authors | Hasan SS / Sun C / Kim AS / Watanabe Y / Chen CL / Klose T / Buda G / Crispin M / Diamond MS / Klimstra WB / Rossmann MG | |||||||||||||||
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_9280.map.gz | 684.6 MB | EMDB map data format | |
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Header (meta data) | emd-9280-v30.xml emd-9280.xml | 19.8 KB 19.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9280_fsc.xml | 23.6 KB | Display | FSC data file |
Images | emd_9280.png | 303.9 KB | ||
Others | emd_9280_half_map_1.map.gz emd_9280_half_map_2.map.gz | 171 MB 171 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9280 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9280 | HTTPS FTP |
-Validation report
Summary document | emd_9280_validation.pdf.gz | 768.1 KB | Display | EMDB validaton report |
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Full document | emd_9280_full_validation.pdf.gz | 767.7 KB | Display | |
Data in XML | emd_9280_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | emd_9280_validation.cif.gz | 38.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9280 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9280 | HTTPS FTP |
-Related structure data
Related structure data | 6mx4MC 9249C 9274C 9275C 9278C 9279C 9281C 6muiC 6mw9C 6mwcC 6mwvC 6mwxC 6mx7C 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_9280.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | EEEV 4.4 Angstrom Full Map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 4.4 Angstrom Half Map 1
File | emd_9280_half_map_1.map | ||||||||||||
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Annotation | EEEV 4.4 Angstrom Half Map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: EEEV 4.4 Angstrom Half Map 2
File | emd_9280_half_map_2.map | ||||||||||||
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Annotation | EEEV 4.4 Angstrom Half Map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Eastern equine encephalitis virus
Entire | Name: Eastern equine encephalitis virus |
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Components |
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-Supramolecule #1: Eastern equine encephalitis virus
Supramolecule | Name: Eastern equine encephalitis virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / NCBI-ID: 11021 / Sci species name: Eastern equine encephalitis virus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: No |
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Host system | Organism: Mesocricetus auratus (golden hamster) / Recombinant cell: BHK-15 |
-Macromolecule #1: E1
Macromolecule | Name: E1 / 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: 47.938141 KDa |
Recombinant expression | Organism: Mesocricetus auratus (golden hamster) |
Sequence | String: YEHTAVMPNK VGIPYKALVE RPGYAPVHLQ IQLVNTRIIP STNLEYITCK YKTKVPSPVV KCCGATQCTS KPHPDYQCQV FTGVYPFMW GGAYCFCDTE NTQMSEAYVE RSEECSIDHA KAYKVHTGTV QAMVNITYGS VSWRSADVYV NGETPAKIGD A KLIIGPLS ...String: YEHTAVMPNK VGIPYKALVE RPGYAPVHLQ IQLVNTRIIP STNLEYITCK YKTKVPSPVV KCCGATQCTS KPHPDYQCQV FTGVYPFMW GGAYCFCDTE NTQMSEAYVE RSEECSIDHA KAYKVHTGTV QAMVNITYGS VSWRSADVYV NGETPAKIGD A KLIIGPLS SAWSPFDNKV VVYGHEVYNY DFPEYGTGKA GSFGDLQSRT STSNDLYANT NLKLQRPQAG IVHTPFTQAP SG FERWKRD KGAPLNDVAP FGCSIALEPL RAENCAVGSI PISIDIPDAA FTRISETPTV SDLECKITEC TYASDFGGIA TVA YKSSKA GNCPIHSPSG VAVIKENDVT LAESGSFTFH FSTANIHPAF KLQVCTSAVT CKGDCKPPKD HIVDYPAQHT ESFT SAISA TAWSWLKVLV GGTSAFIVLG LIATAVVALV LFFHRH |
-Macromolecule #2: E2
Macromolecule | Name: E2 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Eastern equine encephalitis virus |
Molecular weight | Theoretical: 47.046953 KDa |
Recombinant expression | Organism: Mesocricetus auratus (golden hamster) |
Sequence | String: DLDTHFTQYK LARPYIADCP NCGHSRCDSP IAIEEVRGDA HAGVIRIQTS AMFGLKTDGV DLAYMSFMNG KTQKSIKIDN LHVRTSAPC SLVSHHGYYI LAQCPPGDTV TVGFHDGPNR HTCTVAHKVE FRPVGREKYR HPPEHGVELP CNRYTHKRAD Q GHYVEMHQ ...String: DLDTHFTQYK LARPYIADCP NCGHSRCDSP IAIEEVRGDA HAGVIRIQTS AMFGLKTDGV DLAYMSFMNG KTQKSIKIDN LHVRTSAPC SLVSHHGYYI LAQCPPGDTV TVGFHDGPNR HTCTVAHKVE FRPVGREKYR HPPEHGVELP CNRYTHKRAD Q GHYVEMHQ PGLVADHSLL SIHSAKVKIT VPSGAQVKYY CKCPDVREGI TSSDHTTTCT DVKQCRAYLI DNKKWVYNSG RL PRGEGDT FKGKLHVPFV PVKAKCIATL APEPLVEHKH RTLILHLHPD HPTLLTTRSL GSDANPTRQW IERPTTVNFT VTG EGLEYT WGNHPPKRVW AQESGEGNPH GWPHEVVVYY YNRYPLTTII GLCTCVAIIM VSCVTSVWLL CRTRNLCITP YKLA PNAQV PILLALLCCI KPTRA |
-Macromolecule #3: Capsid
Macromolecule | Name: Capsid / type: protein_or_peptide / ID: 3 / 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 |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 4 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-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-6mx4: |