+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22526 | |||||||||
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Title | Subparticle Map of ZIKV MR-766 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / ribonucleoside triphosphate phosphatase activity / membrane => GO:0016020 / double-stranded RNA binding / nucleoside-triphosphate phosphatase / viral capsid / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / ribonucleoside triphosphate phosphatase activity / membrane => GO:0016020 / double-stranded RNA binding / nucleoside-triphosphate phosphatase / viral capsid / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell perinuclear region of cytoplasm / protein dimerization activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / GTP binding / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | ZIKV (virus) / Zika virus | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 3.4 Å | |||||||||
Authors | Jose J / Hafenstein S | |||||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Identification of a pocket factor that is critical to Zika virus assembly. Authors: Nadia M DiNunno / Daniel J Goetschius / Anoop Narayanan / Sydney A Majowicz / Ibrahim Moustafa / Carol M Bator / Susan L Hafenstein / Joyce Jose / Abstract: Zika virus (ZIKV) is an emerging mosquito borne flavivirus and a major public health concern causing severe disease. Due to the presence of a lipid membrane and structural heterogeneity, attaining an ...Zika virus (ZIKV) is an emerging mosquito borne flavivirus and a major public health concern causing severe disease. Due to the presence of a lipid membrane and structural heterogeneity, attaining an atomic resolution structure is challenging, but important to understand virus assembly and life cycle mechanisms that offer distinct targets for therapeutic intervention. We here use subvolume refinement to achieve a 3.4 Å resolution structure and identify two distinct lipid moieties. The first arises from the inner leaflet and is coordinated by hydrophobic residues of the M and E transmembrane helices that form a binding pocket not previously characterized. The second lipid arises from the outer leaflet coordinate between two E protein helices. Structure-based mutagenesis identifies critical hydrophobic interactions and their effect on the virus life cycle. Results show that lipids play an essential role in the ZIKV assembly pathway revealing a potential target of lipid based antiviral drug development. | |||||||||
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_22526.map.gz | 96.2 MB | EMDB map data format | |
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Header (meta data) | emd-22526-v30.xml emd-22526.xml | 10.4 KB 10.4 KB | Display Display | EMDB header |
Images | emd_22526.png | 329.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22526 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22526 | HTTPS FTP |
-Validation report
Summary document | emd_22526_validation.pdf.gz | 531.7 KB | Display | EMDB validaton report |
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Full document | emd_22526_full_validation.pdf.gz | 531.3 KB | Display | |
Data in XML | emd_22526_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | emd_22526_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22526 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22526 | HTTPS FTP |
-Related structure data
Related structure data | 7jyiMC C: citing same article (ref.) M: atomic model generated by this map |
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Similar 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_22526.map.gz / Format: CCP4 / Size: 103 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: 1.1 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 : Zika virus
Entire | Name: Zika virus |
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Components |
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-Supramolecule #1: Zika virus
Supramolecule | Name: Zika virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: propagated in HeLa cells / NCBI-ID: 64320 / Sci species name: Zika virus / Sci species strain: MR-766 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: mosquito (mosquito) |
Virus shell | Shell ID: 1 / Name: Zika / Diameter: 50.0 Å / T number (triangulation number): 3 |
-Macromolecule #1: E Glycoprotein
Macromolecule | Name: E Glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ZIKV (virus) / Strain: MR-766 |
Molecular weight | Theoretical: 54.275836 KDa |
Sequence | String: IRCIGVSNRD FVEGMSGGTW VDVVLEHGGC VTVMAQDKPT VDIELVTTTV SNMAEVRSYC YEASISDMAS DSRCPTQGEA YLDKQSDTQ YVCKRTLVDR GWGNGCGLFG KGSLVTCAKF ACSKKMTGKS IQPENLEYRI MLSVHGSQHS GMIVNDTGYE T DENRAKVE ...String: IRCIGVSNRD FVEGMSGGTW VDVVLEHGGC VTVMAQDKPT VDIELVTTTV SNMAEVRSYC YEASISDMAS DSRCPTQGEA YLDKQSDTQ YVCKRTLVDR GWGNGCGLFG KGSLVTCAKF ACSKKMTGKS IQPENLEYRI MLSVHGSQHS GMIVNDTGYE T DENRAKVE VTPNSPRAEA TLGGFGSLGL DCEPRTGLDF SDLYYLTMNN KHWLVHKEWF HDIPLPWHAG ADTGTPHWNN KE ALVEFKD AHAKRQTVVV LGSQEGAVHT ALAGALEAEM DGAKGKLFSG HLKCRLKMDK LRLKGVSYSL CTAAFTFTKI PAE TLHGTV TVEVQYAGTD GPCKIPVQMA VDMQTLTPVG RLITANPVIT ESTENSKMML ELDPPFGDSY IVIGVGDKKI THHW HRSGS TIGKAFEATV RGAKRMAVLG DTAWDFGSVG GVFNSLGKGI HQIFGAAFKS LFGGMSWFSQ ILIGTLLVWL GLNTK NGSI SLTCLALGGV MIFLSTA |
-Macromolecule #2: M protein
Macromolecule | Name: M protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ZIKV (virus) / Strain: MR-766 |
Molecular weight | Theoretical: 8.555002 KDa |
Sequence | String: AVTLPSHSTR KLQTRSQTWL ESREYTKHLI KVENWIFRNP GFTLVAVAIA WLLGSSTSQK VIYLVMILLI APAYS |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7 |
Staining | Type: NEGATIVE / Material: PTA |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 41.7 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9000 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |