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Yorodumi- EMDB-20199: Symmetric reconstruction of human norovirus GI.1 Norwalk strain V... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20199 | |||||||||
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Title | Symmetric reconstruction of human norovirus GI.1 Norwalk strain VLP in T=3 symmetry | |||||||||
Map data | Symmetric reconstruction of human norovirus GI.1 Norwalk strain VLP in T=3 symmetry | |||||||||
Sample |
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Function / homology | Function and homology information T=3 icosahedral viral capsid / host cell cytoplasm / identical protein binding Similarity search - Function | |||||||||
Biological species | Norovirus Hu/1968/US | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Jung J / Grant T / Thomas DR / Diehnelt CW / Grigorieff N / Joshua-Tor L | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2019 Title: High-resolution cryo-EM structures of outbreak strain human norovirus shells reveal size variations. Authors: James Jung / Timothy Grant / Dennis R Thomas / Chris W Diehnelt / Nikolaus Grigorieff / Leemor Joshua-Tor / Abstract: Noroviruses are a leading cause of foodborne illnesses worldwide. Although GII.4 strains have been responsible for most norovirus outbreaks, the assembled virus shell structures have been available ...Noroviruses are a leading cause of foodborne illnesses worldwide. Although GII.4 strains have been responsible for most norovirus outbreaks, the assembled virus shell structures have been available in detail for only a single strain (GI.1). We present high-resolution (2.6- to 4.1-Å) cryoelectron microscopy (cryo-EM) structures of GII.4, GII.2, GI.7, and GI.1 human norovirus outbreak strain virus-like particles (VLPs). Although norovirus VLPs have been thought to exist in a single-sized assembly, our structures reveal polymorphism between and within genogroups, with small, medium, and large particle sizes observed. Using asymmetric reconstruction, we were able to resolve a Zn metal ion adjacent to the coreceptor binding site, which affected the structural stability of the shell. Our structures serve as valuable templates for facilitating vaccine formulations. | |||||||||
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_20199.map.gz | 1.8 GB | EMDB map data format | |
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Header (meta data) | emd-20199-v30.xml emd-20199.xml | 16.3 KB 16.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20199_fsc.xml | 32.1 KB | Display | FSC data file |
Images | emd_20199.png | 191.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20199 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20199 | HTTPS FTP |
-Validation report
Summary document | emd_20199_validation.pdf.gz | 78.2 KB | Display | EMDB validaton report |
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Full document | emd_20199_full_validation.pdf.gz | 77.3 KB | Display | |
Data in XML | emd_20199_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20199 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20199 | 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_20199.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Symmetric reconstruction of human norovirus GI.1 Norwalk strain VLP in T=3 symmetry | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 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 : Norovirus Hu/1968/US
Entire | Name: Norovirus Hu/1968/US |
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Components |
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-Supramolecule #1: Norovirus Hu/1968/US
Supramolecule | Name: Norovirus Hu/1968/US / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 524364 / Sci species name: Norovirus Hu/1968/US / Sci species strain: GI.1 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: Homo sapiens (human) |
Host system | Organism: Spodoptera frugiperda (fall armyworm) |
Molecular weight | Experimental: 10.19 MDa |
Virus shell | Shell ID: 1 / Name: VP1 / Diameter: 410.0 Å / T number (triangulation number): 3 |
-Macromolecule #1: Human norovirus GI.1 Norwalk strain major capsid (VP1) protein
Macromolecule | Name: Human norovirus GI.1 Norwalk strain major capsid (VP1) protein type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Norovirus Hu/1968/US |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MMMASKDATS SVDGASGAGQ LVPEVNASDP LAMDPVAGSS TAVATAGQVN PIDPWIINNF VQAPQGEFT ISPNNTPGDV LFDLSLGPHL NPFLLHLSQM YNGWVGNMRV RIMLAGNAFT A GKIIVSCI PPGFGSHNLT IAQATLFPHV IADVRTLDPI EVPLEDVRNV ...String: MMMASKDATS SVDGASGAGQ LVPEVNASDP LAMDPVAGSS TAVATAGQVN PIDPWIINNF VQAPQGEFT ISPNNTPGDV LFDLSLGPHL NPFLLHLSQM YNGWVGNMRV RIMLAGNAFT A GKIIVSCI PPGFGSHNLT IAQATLFPHV IADVRTLDPI EVPLEDVRNV LFHNNDRNQQ TM RLVCMLY TPLRTGGGTG DSFVVAGRVM TCPSPDFNFL FLVPPTVEQK TRPFTLPNLP LSS LSNSRA PLPISSMGIS PDNVQSVQFQ NGRCTLDGRL VGTTPVSLSH VAKIRGTSNG TVIN LTELD GTPFHPFEGP APIGFPDLGG CDWHINMTQF GHSSQTQYDV DTTPDTFVPH LGSIQ ANGI GSGNYVGVLS WISPPSHPSG SQVDLWKIPN YGSSITEATH LAPSVYPPGF GEVLVF FMS KMPGPGAYNL PCLLPQEYIS HLASEQAPTV GEAALLHYVD PDTGRNLGEF KAYPDGF LT CVPNGASSGP QQLPINGVFV FVSWVSRFYQ LKPVGTASSA RGRLGLRR |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4 mg/mL |
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Buffer | pH: 5.75 |
Grid | Material: COPPER / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Details: unspecified |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 1820 / Average exposure time: 7.0 sec. / Average electron dose: 78.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |