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Yorodumi- EMDB-42055: Structure of eastern equine encephalitis virus VLP unliganded qua... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42055 | |||||||||
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Title | Structure of eastern equine encephalitis virus VLP unliganded quasi-threefold spike protein | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Eastern Equine Encephalitis Virus / VIRUS LIKE PARTICLE | |||||||||
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: 3.0 Å | |||||||||
Authors | Abraham J / Yang P / Li W / Fan X / Pan J | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structural basis for VLDLR recognition by eastern equine encephalitis virus. Authors: Pan Yang / Wanyu Li / Xiaoyi Fan / Junhua Pan / Colin J Mann / Haley Varnum / Lars E Clark / Sarah A Clark / Adrian Coscia / Himanish Basu / Katherine Nabel Smith / Vesna Brusic / Jonathan Abraham / Abstract: Eastern equine encephalitis virus (EEEV) is the most virulent alphavirus that infects humans, and many survivors develop neurological sequelae, including paralysis and intellectual disability. ...Eastern equine encephalitis virus (EEEV) is the most virulent alphavirus that infects humans, and many survivors develop neurological sequelae, including paralysis and intellectual disability. Alphavirus spike proteins comprise trimers of heterodimers of glycoproteins E2 and E1 that mediate binding to cellular receptors and fusion of virus and host cell membranes during entry. We recently identified very-low density lipoprotein receptor (VLDLR) and apolipoprotein E receptor 2 (ApoER2) as cellular receptors for EEEV and a distantly related alphavirus, Semliki Forest virus (SFV). Here, we use single-particle cryo-electron microscopy (cryo-EM) to determine structures of the EEEV and SFV spike glycoproteins bound to the VLDLR ligand-binding domain and found that EEEV and SFV interact with the same cellular receptor through divergent binding modes. Our studies suggest that the ability of LDLR-related proteins to interact with viral spike proteins through very small footprints with flexible binding modes results in a low evolutionary barrier to the acquisition of LDLR-related proteins as cellular receptors for diverse sets of viruses. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_42055.map.gz | 104.6 MB | EMDB map data format | |
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Header (meta data) | emd-42055-v30.xml emd-42055.xml | 17.8 KB 17.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42055_fsc.xml | 11.1 KB | Display | FSC data file |
Images | emd_42055.png | 62.7 KB | ||
Filedesc metadata | emd-42055.cif.gz | 6.2 KB | ||
Others | emd_42055_half_map_1.map.gz emd_42055_half_map_2.map.gz | 90.6 MB 90.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42055 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42055 | HTTPS FTP |
-Validation report
Summary document | emd_42055_validation.pdf.gz | 966.1 KB | Display | EMDB validaton report |
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Full document | emd_42055_full_validation.pdf.gz | 965.7 KB | Display | |
Data in XML | emd_42055_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | emd_42055_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42055 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42055 | HTTPS FTP |
-Related structure data
Related structure data | 8ua9MC 8ua4C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_42055.map.gz / Format: CCP4 / Size: 115.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_42055_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_42055_half_map_2.map | ||||||||||||
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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: #4 / NCBI-ID: 11021 / Sci species name: Eastern equine encephalitis virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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-Macromolecule #1: Envelope glycoprotein E1
Macromolecule | Name: Envelope glycoprotein E1 / type: protein_or_peptide / ID: 1 / Details: Spike glycoprotein E1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Eastern equine encephalitis virus |
Molecular weight | Theoretical: 47.984246 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: YEHTAVMPNK VGIPYKALVE RPGYAPVHLQ IQLVNTRIIP STNLEYITCK YKTKVPSPVV KCCGATQCTS KPHPDYQCQV FSGVYPFMW GGAYCFCDTE NTQMSEAYVE RSEECSIDHA KAYKVHTGTV QAMVNITYGS VSWRSADVYV NGETPAKIGD A KLIIGPLS ...String: YEHTAVMPNK VGIPYKALVE RPGYAPVHLQ IQLVNTRIIP STNLEYITCK YKTKVPSPVV KCCGATQCTS KPHPDYQCQV FSGVYPFMW GGAYCFCDTE NTQMSEAYVE RSEECSIDHA KAYKVHTGTV QAMVNITYGS VSWRSADVYV NGETPAKIGD A KLIIGPLS SAWSPFDNKV VVYGHEVYNY DFPEYGTGKA GSFGDLQSRT STSNDLYANT NLKLQRPQAG IVHTPFTQVP SG FERWKKD KGAPLNDVAP FGCSIALEPL RAENCAVGSI PISIDIPDAA FTRISETPTV SDLECKITEC TYAFDFGGIA TVA YKSSKA GNCPIHSPSG VAVIKENDVT LAESGSFTFH FSTANIHPAF KLQVCTSAVT CKGDCKPPKD HIVDYPAQHT ESFT SAISA TAWSWIKVLV GGTSAFIVLG LIATAVVALV LFFHRH UniProtKB: Structural polyprotein |
-Macromolecule #2: Structural polyprotein
Macromolecule | Name: Structural polyprotein / 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: 46.818742 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
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 CKCPDVRKGI TSSDHTTTCT DVKQCRAYLI DNKKWVYNSG RL PRGEGDT FKGKLHVPFV PVKAKCIATL APEPLVEHKH RTLILHLHPD HPTLLTTRSL GSDANPTRQW IERPTTVNFT VTG EGLEYT WGNHPPKRVW AQESGEGNPH GWPHEVVVYY YNRYPLTTII GLCTCVAIIM VSCVTSVWLL CRTRNLCITP YKLA PNAQV PILLALLCCI KPT UniProtKB: Structural polyprotein |
-Macromolecule #3: Structural polyprotein
Macromolecule | Name: Structural polyprotein / 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: 6.147061 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: TVMCVLANIT FPCDQPPCMP CCYEKNPHET LTMLEQNYDS RAYDQLLDAA VKCN UniProtKB: Structural polyprotein |
-Macromolecule #4: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Eastern equine encephalitis virus |
Molecular weight | Theoretical: 29.21293 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MFPYPTLNYP PMAPINPMAY RDPNPPRRRW RPFRPPLAAQ IEDLRRSIAN LTLKQRAPNP PAGPPAKRKK PAPSLSLRRK KKRPPPPAK KQKRKPKPGK RQRMCMKLES DKTFPIMLNG QVNGYACVVG GRVFKPLHVE GRIDNEQLAA IKLKKASIYD L EYGDVPQC ...String: MFPYPTLNYP PMAPINPMAY RDPNPPRRRW RPFRPPLAAQ IEDLRRSIAN LTLKQRAPNP PAGPPAKRKK PAPSLSLRRK KKRPPPPAK KQKRKPKPGK RQRMCMKLES DKTFPIMLNG QVNGYACVVG GRVFKPLHVE GRIDNEQLAA IKLKKASIYD L EYGDVPQC MKSDTLQYTS DKPPGFYNWH HGAVQYENNR FTVPRGVGGK GDSGRPILDN KGRVVAIVLG GVNEGSRTAL SV VTWNQKG VTVKDTPEGS EPW UniProtKB: Structural polyprotein |
-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: 9 / 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
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |