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Yorodumi- EMDB-28644: CryoEM structure of Western equine encephalitis virus VLP in comp... -
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-Basic information
Entry | Database: EMDB / ID: EMD-28644 | |||||||||
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Title | CryoEM structure of Western equine encephalitis virus VLP in complex with the avian MXRA8 receptor | |||||||||
Map data | Chikungunya virus-like particle (CHIKV VLP) in complex with a designed MXRA8, a chimera containing D1 from Duck MXRA8 and D2 from Mouse MXRA8. | |||||||||
Sample |
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Keywords | WEEV / MXRA8 / Receptor / Alphavirus / Avian / VLP / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structural Genomics of Infectious Diseases / CSGID / VIRUS LIKE PARTICLE / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information togavirin / T=4 icosahedral viral capsid / 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 ...togavirin / T=4 icosahedral viral capsid / 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 | Chikungunya virus / Anas platyrhynchos (mallard) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.92 Å | |||||||||
Authors | Zimmerman MI / Fremont DH / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Alternate domain repeat usage in an alphavirus entry receptor enables host species expansion Authors: Zimmerman O / Zimmerman MI / Nelson CA / Raju S / Errico JM / Madden EA / Hassan AO / VanBlargan LA / Kim AS / Adams LJ / Basore K / Whitener BM / Earnest JT / Holmes AC / Ebel GD / Zmasek C ...Authors: Zimmerman O / Zimmerman MI / Nelson CA / Raju S / Errico JM / Madden EA / Hassan AO / VanBlargan LA / Kim AS / Adams LJ / Basore K / Whitener BM / Earnest JT / Holmes AC / Ebel GD / Zmasek C / Scheuermann RH / Fremont DH / Diamond MS | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28644.map.gz | 41.4 MB | EMDB map data format | |
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Header (meta data) | emd-28644-v30.xml emd-28644.xml | 17.8 KB 17.8 KB | Display Display | EMDB header |
Images | emd_28644.png | 118.4 KB | ||
Filedesc metadata | emd-28644.cif.gz | 6.5 KB | ||
Others | emd_28644_half_map_1.map.gz emd_28644_half_map_2.map.gz | 77.7 MB 77.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28644 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28644 | HTTPS FTP |
-Related structure data
Related structure data | 8ewfMC 8danC 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_28644.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Chikungunya virus-like particle (CHIKV VLP) in complex with a designed MXRA8, a chimera containing D1 from Duck MXRA8 and D2 from Mouse MXRA8. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.2 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Chikungunya virus-like particle (CHIKV VLP) in complex with...
File | emd_28644_half_map_1.map | ||||||||||||
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Annotation | Chikungunya virus-like particle (CHIKV VLP) in complex with a designed MXRA8, a chimera containing D1 from Duck MXRA8 and D2 from Mouse MXRA8. Half-map A. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Chikungunya virus-like particle (CHIKV VLP) in complex with...
File | emd_28644_half_map_2.map | ||||||||||||
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Annotation | Chikungunya virus-like particle (CHIKV VLP) in complex with a designed MXRA8, a chimera containing D1 from Duck MXRA8 and D2 from Mouse MXRA8. Half-map B. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Chikungunya virus VLP in complex with a chimeric MXRA8 receptor (...
Entire | Name: Chikungunya virus VLP in complex with a chimeric MXRA8 receptor (Avian D1 with Mammalian D2) |
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Components |
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-Supramolecule #1: Chikungunya virus VLP in complex with a chimeric MXRA8 receptor (...
Supramolecule | Name: Chikungunya virus VLP in complex with a chimeric MXRA8 receptor (Avian D1 with Mammalian D2) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Chikungunya virus |
Molecular weight | Theoretical: 495 kDa/nm |
-Macromolecule #1: E1 envelope protein
Macromolecule | Name: E1 envelope protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Chikungunya virus |
Molecular weight | Theoretical: 47.346715 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: YEHVTVIPNT VGVPYKTLVN RPGYSPMVLE MELQSVTLEP TLSLDYITCE YKTVIPSPYV KCCGTAECKD KSLPDYSCKV FTGVYPFMW GGAYCFCDAE NTQLSEAHVE KSESCKTEFA SAYRAHTASA SAKLRVLYQG NNITVAAYAN GDHAVTVKDA K FVVGPMSS ...String: YEHVTVIPNT VGVPYKTLVN RPGYSPMVLE MELQSVTLEP TLSLDYITCE YKTVIPSPYV KCCGTAECKD KSLPDYSCKV FTGVYPFMW GGAYCFCDAE NTQLSEAHVE KSESCKTEFA SAYRAHTASA SAKLRVLYQG NNITVAAYAN GDHAVTVKDA K FVVGPMSS AWTPFDNKIV VYKGDVYNMD YPPFGAGRPG QFGDIQSRTP ESKDVYANTQ LVLQRPAAGT VHVPYSQAPS GF KYWLKER GASLQHTAPF GCQIATNPVR AVNCAVGNIP ISIDIPDAAF TRVVDAPSVT DMSCEVPACT HSSDFGGVAI IKY TASKKG KCAVHSMTNA VTIREADVEV EGNSQLQISF STALASAEFR VQVCSTQVHC AAACHPPKDH IVNYPASHTT LGVQ DISTT AMSWVQKITG GVGLIVAVAA LILIVVLCVS FSRH UniProtKB: Structural polyprotein |
-Macromolecule #2: Spike glycoprotein E2
Macromolecule | Name: Spike glycoprotein E2 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Chikungunya virus |
Molecular weight | Theoretical: 46.858312 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: NFNVYKATRP YLAHCPDCGE GHSCHSPIAL ERIRNEATDG TLKIQVSLQI GIKTDDSHDW TKLRYMDSHT PADAERAGLL VRTSAPCTI TGTMGHFILA RCPKGETLTV GFTDSRKISH TCTHPFHHEP PVIGRERFHS RPQHGKELPC STYVQSTAAT A EEIEVHMP ...String: NFNVYKATRP YLAHCPDCGE GHSCHSPIAL ERIRNEATDG TLKIQVSLQI GIKTDDSHDW TKLRYMDSHT PADAERAGLL VRTSAPCTI TGTMGHFILA RCPKGETLTV GFTDSRKISH TCTHPFHHEP PVIGRERFHS RPQHGKELPC STYVQSTAAT A EEIEVHMP PDTPDRTLMT QQSGNVKITV NGQTVRYKCN CGGSNEGLTT TDKVINNCKI DQCHAAVTNH KNWQYNSPLV PR NAELGDR KGKIHIPFPL ANVTCRVPKA RNPTVTYGKN QVTMLLYPDH PTLLSYRNMG QEPNYHEEWV THKKEVTLTV PTE GLEVTW GNNEPYKYWP QMSTNGTAHG HPHEIILYYY ELYPTMTVVI VSVASFVLLS MVGTAVGMCV CARRRCITPY ELTP GATVP FLLSLLCCVR TTKA UniProtKB: Structural polyprotein |
-Macromolecule #3: Chimeric MXRA8 receptor: D1 from Duck MXRA8 and D2 from Mouse MXRA8
Macromolecule | Name: Chimeric MXRA8 receptor: D1 from Duck MXRA8 and D2 from Mouse MXRA8 type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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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 #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 |
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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: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 1.03 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.5 µm |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.01) / Number images used: 745448 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: ANGULAR RECONSTITUTION |