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Yorodumi- EMDB-42190: Eastern equine encephalitis virus (PE-6) VLP in complex with full... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42190 | |||||||||
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Title | Eastern equine encephalitis virus (PE-6) VLP in complex with full-length VLDLR (asymmetric unit) | |||||||||
Map data | EEEV PE-6 VLP in complex with full-length VLDLR focused reconstruction | |||||||||
Sample | Eastern equine encephalitis virus bound to human VLDLR receptor != Eastern equine encephalitis virus Eastern equine encephalitis virus bound to human VLDLR receptor
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Keywords | virus / receptor / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information reelin receptor activity / VLDL clearance / glycoprotein transport / very-low-density lipoprotein particle binding / ventral spinal cord development / very-low-density lipoprotein particle receptor activity / Reelin signalling pathway / reelin-mediated signaling pathway / low-density lipoprotein particle receptor activity / very-low-density lipoprotein particle clearance ...reelin receptor activity / VLDL clearance / glycoprotein transport / very-low-density lipoprotein particle binding / ventral spinal cord development / very-low-density lipoprotein particle receptor activity / Reelin signalling pathway / reelin-mediated signaling pathway / low-density lipoprotein particle receptor activity / very-low-density lipoprotein particle clearance / very-low-density lipoprotein particle / T=4 icosahedral viral capsid / positive regulation of dendrite development / dendrite morphogenesis / cargo receptor activity / lipid transport / apolipoprotein binding / clathrin-coated pit / cholesterol metabolic process / VLDLR internalisation and degradation / receptor-mediated endocytosis / memory / calcium-dependent protein binding / nervous system development / host cell cytoplasm / receptor complex / symbiont entry into host cell / lysosomal membrane / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / calcium ion binding / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / signal transduction / proteolysis / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Eastern equine encephalitis virus / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.89 Å | |||||||||
Authors | Adams LJ / Fremont DH | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Cell / Year: 2024 Title: Structural and functional basis of VLDLR usage by Eastern equine encephalitis virus. Authors: Lucas J Adams / Saravanan Raju / Hongming Ma / Theron Gilliland / Douglas S Reed / William B Klimstra / Daved H Fremont / Michael S Diamond / Abstract: The very-low-density lipoprotein receptor (VLDLR) comprises eight LDLR type A (LA) domains and supports entry of distantly related alphaviruses, including Eastern equine encephalitis virus (EEEV) and ...The very-low-density lipoprotein receptor (VLDLR) comprises eight LDLR type A (LA) domains and supports entry of distantly related alphaviruses, including Eastern equine encephalitis virus (EEEV) and Semliki Forest virus (SFV). Here, by resolving multiple cryo-electron microscopy structures of EEEV-VLDLR complexes and performing mutagenesis and functional studies, we show that EEEV uses multiple sites (E1/E2 cleft and E2 A domain) to engage more than one LA domain simultaneously. However, no single LA domain is necessary or sufficient to support efficient EEEV infection. Whereas all EEEV strains show conservation of two VLDLR-binding sites, the EEEV PE-6 strain and a few other EEE complex members feature a single amino acid substitution that enables binding of LA domains to an additional site on the E2 B domain. These structural and functional analyses informed the design of a minimal VLDLR decoy receptor that neutralizes EEEV infection and protects mice from lethal challenge. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_42190.map.gz | 63.3 MB | EMDB map data format | |
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Header (meta data) | emd-42190-v30.xml emd-42190.xml | 21.4 KB 21.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42190_fsc.xml | 9.2 KB | Display | FSC data file |
Images | emd_42190.png | 48 KB | ||
Filedesc metadata | emd-42190.cif.gz | 6.8 KB | ||
Others | emd_42190_additional_1.map.gz emd_42190_half_map_1.map.gz emd_42190_half_map_2.map.gz | 33.1 MB 62.2 MB 62.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42190 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42190 | HTTPS FTP |
-Validation report
Summary document | emd_42190_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_42190_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_42190_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | emd_42190_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42190 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42190 | HTTPS FTP |
-Related structure data
Related structure data | 8ufbMC 8ufaC 8ufcC 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_42190.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | EEEV PE-6 VLP in complex with full-length VLDLR focused reconstruction | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.081 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: EEEV PE-6 VLP in complex with full-length VLDLR...
File | emd_42190_additional_1.map | ||||||||||||
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Annotation | EEEV PE-6 VLP in complex with full-length VLDLR focused reconstruction (unsharpened map) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: EEEV PE-6 VLP in complex with full-length VLDLR...
File | emd_42190_half_map_1.map | ||||||||||||
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Annotation | EEEV PE-6 VLP in complex with full-length VLDLR focused reconstruction (half map A) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: EEEV PE-6 VLP in complex with full-length VLDLR...
File | emd_42190_half_map_2.map | ||||||||||||
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Annotation | EEEV PE-6 VLP in complex with full-length VLDLR focused reconstruction (half map B) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Eastern equine encephalitis virus bound to human VLDLR receptor
Entire | Name: Eastern equine encephalitis virus bound to human VLDLR receptor |
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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-#4 / Details: Virus-like particle bound to human VLDLR receptor / NCBI-ID: 11021 / Sci species name: Eastern equine encephalitis virus / Sci species strain: PE-6 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: Yes |
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-Macromolecule #1: E1 protein
Macromolecule | Name: E1 protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Eastern equine encephalitis virus / Strain: PE-6 |
Molecular weight | Theoretical: 47.93518 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: YEHTAVMPNK VGIPYKALVE RPGYAPVHLQ IQLVNTRIIP STNLEYITCK YKTKVPSPVV KCCGATQCTS KPHPDYQCQV FSGVYPFMY GGAYCFCDTE NTQMSEAYVE RSEECSIDHA KAYKVHTGTV QAMVNITYGS VSWRSADVYV NGETPAKIGD A KLIIGPLS ...String: YEHTAVMPNK VGIPYKALVE RPGYAPVHLQ IQLVNTRIIP STNLEYITCK YKTKVPSPVV KCCGATQCTS KPHPDYQCQV FSGVYPFMY 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 HIVDYAAQHT ESFT SAISA TAWSWIKVLV GGTSAFIVLG LIATAVVALV LFFHRH UniProtKB: Structural polyprotein |
-Macromolecule #2: E2 protein
Macromolecule | Name: E2 protein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Eastern equine encephalitis virus / Strain: PE-6 |
Molecular weight | Theoretical: 46.378191 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 PILLALLCC UniProtKB: Structural polyprotein |
-Macromolecule #3: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Eastern equine encephalitis virus / Strain: PE-6 |
Molecular weight | Theoretical: 16.540656 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DKTFPIMLNG QVNGYACVVG GRVFKPLHVE GRIDNEQLAA IKLKKASIYD LEYGDVPQCM KSDTLQYTSD KPPGFYNWHH GAVQYENNR FTVPRGVGGK GDSGRPILDN KGRVVAIVLG GVNEGSRTAL SVVTWNQKGV TVKDTPEGSE PW UniProtKB: Structural polyprotein |
-Macromolecule #4: Isoform Short of Very low-density lipoprotein receptor
Macromolecule | Name: Isoform Short of Very low-density lipoprotein receptor type: protein_or_peptide / ID: 4 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 82.9995 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GRKAKCEPSQ FQCTNGRCIT LLWKCDGDED CVDGSDEKNC VKKTCAESDF VCNNGQCVPS RWKCDGDPDC EDGSDESPEQ CHMRTCRIH EISCGAHSTQ CIPVSWRCDG ENDCDSGEDE ENCGNITCSP DEFTCSSGRC ISRNFVCNGQ DDCSDGSDEL D CAPPTCGA ...String: GRKAKCEPSQ FQCTNGRCIT LLWKCDGDED CVDGSDEKNC VKKTCAESDF VCNNGQCVPS RWKCDGDPDC EDGSDESPEQ CHMRTCRIH EISCGAHSTQ CIPVSWRCDG ENDCDSGEDE ENCGNITCSP DEFTCSSGRC ISRNFVCNGQ DDCSDGSDEL D CAPPTCGA HEFQCSTSSC IPISWVCDDD ADCSDQSDES LEQCGRQPVI HTKCPASEIQ CGSGECIHKK WRCDGDPDCK DG SDEVNCP SRTCRPDQFE CEDGSCIHGS RQCNGIRDCV DGSDEVNCKN VNQCLGPGKF KCRSGECIDI SKVCNQEQDC RDW SDEPLK ECHINECLVN NGGCSHICKD LVIGYECDCA AGFELIDRKT CGDIDECQNP GICSQICINL KGGYKCECSR GYQM DLATG VCKAVGKEPS LIFTNRRDIR KIGLERKEYI QLVEQLRNTV ALDADIAAQK LFWADLSQKA IFSASIDDKV GRHVK MIDN VYNPAAIAVD WVYKTIYWTD AASKTISVAT LDGTKRKFLF NSDLREPASI AVDPLSGFVY WSDWGEPAKI EKAGMN GFD RRPLVTADIQ WPNGITLDLI KSRLYWLDSK LHMLSSVDLN GQDRRIVLKS LEFLAHPLAL TIFEDRVYWI DGENEAV YG ANKFTGSELA TLVNNLNDAQ DIIVYHELVQ PSGKNWCEED MENGGCEYLC LPAPQINDHS PKYTCSCPSG YNVEENGR D CQRINVTTAV SEVSVPPKGT SHHHHHH UniProtKB: Very low-density lipoprotein receptor |
-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: 8 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #6: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 12 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 37.9 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: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |