+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23273 | |||||||||
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Title | The mature Usutu SAAR-1776, Map B | |||||||||
Map data | Usutu Map B | |||||||||
Sample |
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Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / membrane => GO:0016020 / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / membrane => GO:0016020 / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / serine-type endopeptidase activity / viral RNA genome replication / RNA-dependent RNA polymerase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / proteolysis / extracellular region / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Usutu virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.35 Å | |||||||||
Authors | Khare B / Klose T / Fang Q / Kuhn R | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2021 Title: Structure of Usutu virus SAAR-1776 displays fusion loop asymmetry. Authors: Baldeep Khare / Thomas Klose / Qianglin Fang / Michael G Rossmann / Richard J Kuhn / Abstract: Usutu virus (USUV) is an emerging arbovirus in Europe that has been increasingly identified in asymptomatic humans and donated blood samples and is a cause of increased incidents of neuroinvasive ...Usutu virus (USUV) is an emerging arbovirus in Europe that has been increasingly identified in asymptomatic humans and donated blood samples and is a cause of increased incidents of neuroinvasive human disease. Treatment or prevention options for USUV disease are currently nonexistent, the result of a lack of understanding of the fundamental elements of USUV pathogenesis. Here, we report two structures of the mature USUV virus, determined at a resolution of 2.4 Å, using single-particle cryogenic electron microscopy. Mature USUV is an icosahedral shell of 180 copies of envelope (E) and membrane (M) proteins arranged in the classic herringbone pattern. However, unlike previous reports of flavivirus structures, we observe virus subpopulations and differences in the fusion loop disulfide bond. Presence of a second, unique E glycosylation site could elucidate host interactions, contributing to the broad USUV tissue tropism. The structures provide a basis for exploring USUV interactions with glycosaminoglycans and lectins, the role of the RGD motif as a receptor, and the inability of West Nile virus therapeutic antibody E16 to neutralize the mature USUV strain SAAR-1776. Finally, we identify three lipid binding sites and predict key residues that likely participate in virus stability and flexibility during membrane fusion. Our findings provide a framework for the development of USUV therapeutics and expand the current knowledge base of flavivirus biology. | |||||||||
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_23273.map.gz | 3.1 GB | EMDB map data format | |
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Header (meta data) | emd-23273-v30.xml emd-23273.xml | 16.8 KB 16.8 KB | Display Display | EMDB header |
Images | emd_23273.png | 267 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23273 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23273 | HTTPS FTP |
-Validation report
Summary document | emd_23273_validation.pdf.gz | 643 KB | Display | EMDB validaton report |
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Full document | emd_23273_full_validation.pdf.gz | 642.6 KB | Display | |
Data in XML | emd_23273_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | emd_23273_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23273 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23273 | HTTPS FTP |
-Related structure data
Related structure data | 7lchMC 7lcgC 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_23273.map.gz / Format: CCP4 / Size: 3.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Usutu Map B | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.664 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 : Usutu virus
Entire | Name: Usutu virus |
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Components |
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-Supramolecule #1: Usutu virus
Supramolecule | Name: Usutu virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: Virus purified using Vero cells. / NCBI-ID: 64286 / Sci species name: Usutu virus / Sci species strain: SAAR-1776 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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Host (natural) | Organism: Turdus merula (blackbird) |
Host system | Organism: Chlorocebus aethiops (grivet) / Recombinant cell: Vero cells |
-Macromolecule #1: Envelope protein E
Macromolecule | Name: Envelope protein E / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Usutu virus / Strain: SAAR-1776 |
Molecular weight | Theoretical: 53.623812 KDa |
Recombinant expression | Organism: Chlorocebus aethiops (grivet) |
Sequence | String: FNCLGMSNRD FLEGVSGATW VDVVLEGDSC ITIMAKDKPT IDIKMMETEA TNLAEVRSYC YLATVSDVST VSNCPTTGEA HNPKRAEDT YVCKSGVTDR GWGNGCGLFG KGSIDTCANF TCSLKAVGRM IQPENVKYEV GIFIHGSTSS DTHGNYSSQL G ASQAGRFT ...String: FNCLGMSNRD FLEGVSGATW VDVVLEGDSC ITIMAKDKPT IDIKMMETEA TNLAEVRSYC YLATVSDVST VSNCPTTGEA HNPKRAEDT YVCKSGVTDR GWGNGCGLFG KGSIDTCANF TCSLKAVGRM IQPENVKYEV GIFIHGSTSS DTHGNYSSQL G ASQAGRFT ITPNSPAITV KMGDYGEISV ECEPRNGLNT EAYYIMSVGT KHFLVHREWF NDLALPWTSP ASSNWRNREI LL EFEEPHA TKQSVVALGS QEGALHQALA GAVPVSFSSS VKLTSGHLKC RVKMEKLTLK GTTYGMCTEK FSFAKNPADT GHS TVVLEL QYTGSDGPCK IPISIVASLS DLTPIGRMVT ANPYVASSEA NAKVLVEMEP PFGDSYIVVG RGDKQINHHW HKAG SSIGK AFITTIKGAQ RLAALGDPAW DFGSVGGIFN SVGKAVHQVF GGAFRTLFGG MSWITQGLMG ALLLWMGVNA RDRSI ALVM LATGGVLLFL ATSVHA |
-Macromolecule #2: Membrane protein M
Macromolecule | Name: Membrane protein M / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Usutu virus / Strain: SAAR-1776 |
Molecular weight | Theoretical: 8.33371 KDa |
Recombinant expression | Organism: Chlorocebus aethiops (grivet) |
Sequence | String: SIAVQTHGES MLANKKDAWL DSTKASRYLM KTENWIIRNP GYAFVAVLLG WMLGSNNGQR VVFVVLLLLV APAYS |
-Macromolecule #3: TRIMETHYL-[2-[[(2S,3S)-2-(OCTADECANOYLAMINO)-3-OXIDANYL-BUTOXY]-O...
Macromolecule | Name: TRIMETHYL-[2-[[(2S,3S)-2-(OCTADECANOYLAMINO)-3-OXIDANYL-BUTOXY]-OXIDANYL-PHOSPHORYL]OXYETHYL]AZANIUM type: ligand / ID: 3 / Number of copies: 3 / Formula: 0SM |
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Molecular weight | Theoretical: 537.733 Da |
Chemical component information | ChemComp-0SM: |
-Macromolecule #4: (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5...
Macromolecule | Name: (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE type: ligand / ID: 4 / Number of copies: 3 / Formula: PC7 |
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Molecular weight | Theoretical: 763.1 Da |
Chemical component information | ChemComp-PC7: |
-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: 6 / 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 Component:
Details: 20 mM Tris, 120 mM NaCl, 1 mM EDTA, pH 8.0 | ||||||||||||
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Grid | Model: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER | ||||||||||||
Vitrification | Cryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 3689 / Average exposure time: 2.08 sec. / Average electron dose: 23.68 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 64000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | PDB-7lch: |