[English] 日本語
Yorodumi- EMDB-40711: CryoEM structure of Western equine encephalitis virus VLP in comp... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40711 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CryoEM structure of Western equine encephalitis virus VLP in complex with the chimeric Du-D1-Mo-D2 MXRA8 receptor | |||||||||
Map data | Density map of WEEV-VLP in complex with a chimeric Duck-D1-Mouse-D2 (DuD1-MoD2) MXRA8. | |||||||||
Sample |
| |||||||||
Keywords | WEEV / MXRA8 / Receptor / Alphavirus / Avian / VLP / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structural Genomics of Infectious Diseases / CSGID / VIRAL PROTEIN-SIGNALING PROTEIN complex | |||||||||
Function / homology | Function and homology information T=4 icosahedral viral capsid / host cell cytoplasm / 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 / virion membrane / structural molecule activity / proteolysis ...T=4 icosahedral viral capsid / host cell cytoplasm / 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 / virion membrane / structural molecule activity / proteolysis / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Western equine encephalitis virus / Anas platyrhynchos (mallard) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.89 Å | |||||||||
Authors | Zimmerman MI / Fremont DH / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: Cell / Year: 2023 Title: Vertebrate-class-specific binding modes of the alphavirus receptor MXRA8. Authors: Ofer Zimmerman / Maxwell I Zimmerman / Saravanan Raju / Christopher A Nelson / John M Errico / Emily A Madden / Autumn C Holmes / Ahmed O Hassan / Laura A VanBlargan / Arthur S Kim / Lucas J ...Authors: Ofer Zimmerman / Maxwell I Zimmerman / Saravanan Raju / Christopher A Nelson / John M Errico / Emily A Madden / Autumn C Holmes / Ahmed O Hassan / Laura A VanBlargan / Arthur S Kim / Lucas J Adams / Katherine Basore / Bradley M Whitener / Sathvik Palakurty / Hannah G Davis-Adams / Chengqun Sun / Theron Gilliland / James T Earnest / Hongming Ma / Gregory D Ebel / Christian Zmasek / Richard H Scheuermann / William B Klimstra / Daved H Fremont / Michael S Diamond / Abstract: MXRA8 is a receptor for chikungunya (CHIKV) and other arthritogenic alphaviruses with mammalian hosts. However, mammalian MXRA8 does not bind to alphaviruses that infect humans and have avian ...MXRA8 is a receptor for chikungunya (CHIKV) and other arthritogenic alphaviruses with mammalian hosts. However, mammalian MXRA8 does not bind to alphaviruses that infect humans and have avian reservoirs. Here, we show that avian, but not mammalian, MXRA8 can act as a receptor for Sindbis, western equine encephalitis (WEEV), and related alphaviruses with avian reservoirs. Structural analysis of duck MXRA8 complexed with WEEV reveals an inverted binding mode compared with mammalian MXRA8 bound to CHIKV. Whereas both domains of mammalian MXRA8 bind CHIKV E1 and E2, only domain 1 of avian MXRA8 engages WEEV E1, and no appreciable contacts are made with WEEV E2. Using these results, we generated a chimeric avian-mammalian MXRA8 decoy-receptor that neutralizes infection of multiple alphaviruses from distinct antigenic groups in vitro and in vivo. Thus, different alphaviruses can bind MXRA8 encoded by different vertebrate classes with distinct engagement modes, which enables development of broad-spectrum inhibitors. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_40711.map.gz | 4.5 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-40711-v30.xml emd-40711.xml | 18.4 KB 18.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40711_fsc.xml | 9.2 KB | Display | FSC data file |
Images | emd_40711.png | 290 KB | ||
Filedesc metadata | emd-40711.cif.gz | 6.5 KB | ||
Others | emd_40711_half_map_1.map.gz emd_40711_half_map_2.map.gz | 77.6 MB 77.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40711 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40711 | HTTPS FTP |
-Related structure data
Related structure data | 8sqnMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_40711.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Density map of WEEV-VLP in complex with a chimeric Duck-D1-Mouse-D2 (DuD1-MoD2) MXRA8. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.2 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: Density half map A of WEEV-VLP in complex...
File | emd_40711_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Density half map A of WEEV-VLP in complex with a chimeric Duck-D1-Mouse-D2 (DuD1-MoD2) MXRA8. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Density half map B of WEEV-VLP in complex...
File | emd_40711_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Density half map B of WEEV-VLP in complex with a chimeric Duck-D1-Mouse-D2 (DuD1-MoD2) MXRA8. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Western equine encephalitis virus VLP in complex with a chimeric ...
Entire | Name: Western equine encephalitis virus VLP in complex with a chimeric MXRA8 receptor (Avian D1 with Mammalian D2) |
---|---|
Components |
|
-Supramolecule #1: Western equine encephalitis virus VLP in complex with a chimeric ...
Supramolecule | Name: Western equine encephalitis virus VLP in complex with a chimeric MXRA8 receptor (Avian D1 with Mammalian D2) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
---|---|
Source (natural) | Organism: Western equine encephalitis virus |
Molecular weight | Theoretical: 7.45 MDa |
-Macromolecule #1: DuD1MoD2 chimeric MXRA8
Macromolecule | Name: DuD1MoD2 chimeric MXRA8 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Anas platyrhynchos (mallard) |
Molecular weight | Theoretical: 30.539193 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: SSSLVSESVV SLAAGTQAVL RCQSPRMVWT QDRLNDRQRV VHWDVYSTYY GDNKMERLCD MYSAGDQRVY SSYNQGRIFM PQNAFTDGN FSLVIKDVAE SDGGIYSCNL HHHYCHLYET VKIQLDVTKK AKAAKEYWDG EKAVIVALEG STVMLPCVNR N QIWTERHL ...String: SSSLVSESVV SLAAGTQAVL RCQSPRMVWT QDRLNDRQRV VHWDVYSTYY GDNKMERLCD MYSAGDQRVY SSYNQGRIFM PQNAFTDGN FSLVIKDVAE SDGGIYSCNL HHHYCHLYET VKIQLDVTKK AKAAKEYWDG EKAVIVALEG STVMLPCVNR N QIWTERHL EEAQQVVHWD RQLPGVSHDR ADRLLDLYAS GERRAYGPPF LRDRVSVNTN AFARGDFSLR IDELERADEG IY SCHLHHH YCGLHERRVF HLQVTEPA |
-Macromolecule #2: E1 envelope glycoprotein
Macromolecule | Name: E1 envelope glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Western equine encephalitis virus |
Molecular weight | Theoretical: 47.188562 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: FEHATTVPNV PGIPYKALVE RAGYAPLNLE ITVVSSELTP STNKEYVTCK FHTVVPSPQV KCCGSLECKA SSKADYTCRV FGGVYPFMW GGAQCFCDSE NTQLSEAYVE FAPDCTIDHA VALKVHTAAL KVGLRIVYGN TTARLDTFVN GVTPGSSRDL K VIAGPISA ...String: FEHATTVPNV PGIPYKALVE RAGYAPLNLE ITVVSSELTP STNKEYVTCK FHTVVPSPQV KCCGSLECKA SSKADYTCRV FGGVYPFMW GGAQCFCDSE NTQLSEAYVE FAPDCTIDHA VALKVHTAAL KVGLRIVYGN TTARLDTFVN GVTPGSSRDL K VIAGPISA AFSPFDHKVV IRKGLVYNYD FPEYGAMNPG AFGDIQASSL DATDIVARTD IRLLKPSVKN IHVPYTQAVS GY EMWKNNS GRPLQETAPF GCKIEVEPLR ATNCAYGHIP ISIDIPDAAF VRSSESPTIL EVSCTVADCI YSADFGGSLT LQY KANREG HCPVHSHSTT AVLKEATTHV TATGSITLHF STSSPQANFI VSLCGKKTTC NAECKPPADH IIGEPHKVDQ EFQA AVSKT SWNWLLALFG GASSLIVVGL IVLVCSSMLI NTR UniProtKB: Structural polyprotein |
-Macromolecule #3: E2 envelope glycoprotein
Macromolecule | Name: E2 envelope glycoprotein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Western equine encephalitis virus |
Molecular weight | Theoretical: 46.171617 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: ITDDFTLTSP YLGFCPYCRH SAPCFSPIKI ENVWDESDDG SIRIQVSAQF GYNQAGTADV TKFRYMSYDH DHDIKEDSME KLAISTSGP CRRLGHKGYF LLAQCPPGDS VTVSITSGAS ENSCTVEKKI RRKFVGREEY LFPPVHGKLV KCHVYDHLKE T SAGYITMH ...String: ITDDFTLTSP YLGFCPYCRH SAPCFSPIKI ENVWDESDDG SIRIQVSAQF GYNQAGTADV TKFRYMSYDH DHDIKEDSME KLAISTSGP CRRLGHKGYF LLAQCPPGDS VTVSITSGAS ENSCTVEKKI RRKFVGREEY LFPPVHGKLV KCHVYDHLKE T SAGYITMH RPGPHAYKSY LEEASGEVYI KPPSGKNVTY ECKCGDYSTG IVSTRTKMNG CTKAKQCIAY KRDQTKWVFN SP DLIRHTD HSVQGKLHIP FRLTPTVCPV PLAHTPTVTK WFKGITLHLT ATRPTLLTTR KLGLRADATA EWITGTTSRN FSV GREGLE YVWGNHEPVR VWAQESAPGD PHGWPHEIII HYYHRHPVYT VIVLCGVALA ILVGTASSAA CIAKARRDCL TPYA LAPNA TVPTALAVLC UniProtKB: Structural polyprotein |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 9 / Formula: NAG |
---|---|
Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS GLACIOS |
---|---|
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.5 µm |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 46.45 e/Å2 |