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Yorodumi- EMDB-24394: Unsharpened electron microscopy map of Venezuelan equine encephal... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24394 | |||||||||
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Title | Unsharpened electron microscopy map of Venezuelan equine encephalitis VLP in complex with Domains 1 and 2 of LDLRAD3 receptor | |||||||||
Map data | Unsharpened electron microscopy map of Venezuelan equine encephalitis VLP in complex with Domains 1 and 2 of LDLRAD3 receptor | |||||||||
Sample |
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Keywords | VEEV / viral envelope / host receptor / low-density lipoprotein receptor type-A module / LDLRAD3 / encephalitic alphavirus / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / VIRUS LIKE PARTICLE | |||||||||
Function / homology | Function and homology information regulation of protein processing / T=4 icosahedral viral capsid / receptor-mediated endocytosis / amyloid-beta binding / host cell cytoplasm / membrane => GO:0016020 / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell ...regulation of protein processing / T=4 icosahedral viral capsid / receptor-mediated endocytosis / amyloid-beta binding / host cell cytoplasm / membrane => GO:0016020 / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) / Venezuelan equine encephalitis virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.97 Å | |||||||||
Authors | Basore K / Nelson CA / Fremont DH | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nature / Year: 2021 Title: Structure of Venezuelan equine encephalitis virus in complex with the LDLRAD3 receptor. Authors: Katherine Basore / Hongming Ma / Natasha M Kafai / Samantha Mackin / Arthur S Kim / Christopher A Nelson / Michael S Diamond / Daved H Fremont / Abstract: LDLRAD3 is a recently defined attachment and entry receptor for Venezuelan equine encephalitis virus (VEEV), a New World alphavirus that causes severe neurological disease in humans. Here we present ...LDLRAD3 is a recently defined attachment and entry receptor for Venezuelan equine encephalitis virus (VEEV), a New World alphavirus that causes severe neurological disease in humans. Here we present near-atomic-resolution cryo-electron microscopy reconstructions of VEEV virus-like particles alone and in a complex with the ectodomains of LDLRAD3. Domain 1 of LDLRAD3 is a low-density lipoprotein receptor type-A module that binds to VEEV by wedging into a cleft created by two adjacent E2-E1 heterodimers in one trimeric spike, and engages domains A and B of E2 and the fusion loop in E1. Atomic modelling of this interface is supported by mutagenesis and anti-VEEV antibody binding competition assays. Notably, VEEV engages LDLRAD3 in a manner that is similar to the way that arthritogenic alphaviruses bind to the structurally unrelated MXRA8 receptor, but with a much smaller interface. These studies further elucidate the structural basis of alphavirus-receptor interactions, which could inform the development of therapies to mitigate infection and disease against multiple members of this family. | |||||||||
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_24394.map.gz | 1.3 GB | EMDB map data format | |
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Header (meta data) | emd-24394-v30.xml emd-24394.xml | 15.8 KB 15.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_24394_fsc.xml | 26.6 KB | Display | FSC data file |
Images | emd_24394.png | 221.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24394 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24394 | HTTPS FTP |
-Validation report
Summary document | emd_24394_validation.pdf.gz | 696.6 KB | Display | EMDB validaton report |
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Full document | emd_24394_full_validation.pdf.gz | 696.2 KB | Display | |
Data in XML | emd_24394_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | emd_24394_validation.cif.gz | 28.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24394 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24394 | HTTPS FTP |
-Related 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_24394.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Unsharpened electron microscopy map of Venezuelan equine encephalitis VLP in complex with Domains 1 and 2 of LDLRAD3 receptor | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Venezuelan equine encephalitis VLP in complex with domains 1 and ...
Entire | Name: Venezuelan equine encephalitis VLP in complex with domains 1 and 2 of the LDLRAD3 receptor |
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Components |
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-Supramolecule #1: Venezuelan equine encephalitis VLP in complex with domains 1 and ...
Supramolecule | Name: Venezuelan equine encephalitis VLP in complex with domains 1 and 2 of the LDLRAD3 receptor type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Supramolecule #2: Venezuelan equine encephalitis VLP
Supramolecule | Name: Venezuelan equine encephalitis VLP / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3 Details: Virus like particle produce in HEK293F cells by recombinant expression of structural proteins. |
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Source (natural) | Organism: Venezuelan equine encephalitis virus |
-Supramolecule #3: LDLRAD3 receptor domains 1 and 2
Supramolecule | Name: LDLRAD3 receptor domains 1 and 2 / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #4 Details: Receptor fragment produced asserted Fc fusion in Expi293F cells and released by HRV 3C Cleavage. |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Macromolecule #1: E1 envelope glycoprotein
Macromolecule | Name: E1 envelope glycoprotein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Venezuelan equine encephalitis virus / Strain: TC-83 |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: YEHATTMPSQ AGISYNTIVN RAGYAPLPIS ITPTKIKLIP TVNLEYVTCH YKTGMDSPAI KCCGSQECTP TYRPDEQCKV FTGVYPFMW GGAYCFCDTE NTQVSKAYVM KSDDCLADHA EAYKAHTASV QAFLNITVGE HSIVTTVYVN GETPVNFNGV K ITAGPLST ...String: YEHATTMPSQ AGISYNTIVN RAGYAPLPIS ITPTKIKLIP TVNLEYVTCH YKTGMDSPAI KCCGSQECTP TYRPDEQCKV FTGVYPFMW GGAYCFCDTE NTQVSKAYVM KSDDCLADHA EAYKAHTASV QAFLNITVGE HSIVTTVYVN GETPVNFNGV K ITAGPLST AWTPFDRKIV QYAGEIYNYD FPEYGAGQPG AFGDIQSRTV SSSDLYANTN LVLQRPKAGA IHVPYTQAPS GF EQWKKDK APSLKFTAPF GCEIYTNPIR AENCAVGSIP LAFDIPDALF TRVSETPTLS AAECTLNECV YSSDFGGIAT VKY SASKSG KCAVHVPSGT ATLKEAAVEL TEQGSATIHF STANIHPEFR LQICTSYVTC KGDCHPPKDH IVTHPQYHAQ TFTA AVSKT AWTWLTSLLG GSAVIIIIGL VLATIVAMYV LTNQKHN |
-Macromolecule #2: E2 envelope glycoprotein
Macromolecule | Name: E2 envelope glycoprotein / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Venezuelan equine encephalitis virus / Strain: TC-83 |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: STEELFNEYK LTRPYMARCI RCAVGSCHSP IAIEAVKSDG HDGYVRLQTS SQYGLDSSGN LKGRTMRYDM HGTIKEIPLH QVSLYTSRP CHIVDGHGYF LLARCPAGDS ITMEFKKDSV RHSCSVPYEV KFNPVGRELY THPPEHGVEQ ACQVYAHDAQ N RGAYVEMH ...String: STEELFNEYK LTRPYMARCI RCAVGSCHSP IAIEAVKSDG HDGYVRLQTS SQYGLDSSGN LKGRTMRYDM HGTIKEIPLH QVSLYTSRP CHIVDGHGYF LLARCPAGDS ITMEFKKDSV RHSCSVPYEV KFNPVGRELY THPPEHGVEQ ACQVYAHDAQ N RGAYVEMH LPGSEVDSSL VSLSGSSVTV TPPDGTSALV ECECGGTKIS ETINKTKQFS QCTKKEQCRA YRLQNDKWVY NS DKLPKAA GATLKGKLHV PFLLADGKCT VPLAPEPMIT FGFRSVSLKL HPKNPTYLIT RQLADEPHYT HELISEPAVR NFT VTEKGW EFVWGNHPPK RFWAQETAPG NPHGLPHEVI THYYHRYPMS TILGLSICAA IATVSVAAST WLFCRSRVAC LTPY RLTPN ARIPFCLAVL CCARTARA |
-Macromolecule #3: Capsid
Macromolecule | Name: Capsid / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Venezuelan equine encephalitis virus / Strain: TC-83 |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: KRQRMVMKLE SDKTFPIMLE GKINGYACVV GGKLFRPMHV EGKIDNDVLA ALKTKKASKY DLEYADVPQN MRADTFKYTH EKPQGYYSW HHGAVQYENG RFTVPKGVGA KGDSGRPILD NQGRVVAIVL GGVNEGSRTA LSVVMWNEKG VTVKYTPENC E QW |
-Macromolecule #4: Low-density lipoprotein receptor class A domain-containing protein 3
Macromolecule | Name: Low-density lipoprotein receptor class A domain-containing protein 3 type: protein_or_peptide / ID: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QLLPGNNFTN ECNIPGNFMC SNGRCIPGAW QCDGLPDCFD KSDEKECPKA KSKCGPTFFP CASGIHCIIG RFRCNGFEDC PDGSDEENCT ANPLLL |
-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: 35.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |