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Yorodumi- EMDB-20197: Symmetric reconstruction of human norovirus GI.7 Houston strain V... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20197 | |||||||||
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Title | Symmetric reconstruction of human norovirus GI.7 Houston strain VLP in T=3 symmetry | |||||||||
Map data | Symmetric reconstruction of human norovirus GI.7 Houston strain in T=3 symmetry | |||||||||
Sample |
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Function / homology | Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Viral coat protein subunit / Major capsid protein Function and homology information | |||||||||
Biological species | Norovirus Hu/GI.7/TCH-060/USA/2003 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 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_20197.map.gz | 1.8 GB | EMDB map data format | |
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Header (meta data) | emd-20197-v30.xml emd-20197.xml | 15.8 KB 15.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20197_fsc.xml | 32.1 KB | Display | FSC data file |
Images | emd_20197.png | 196.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20197 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20197 | HTTPS FTP |
-Validation report
Summary document | emd_20197_validation.pdf.gz | 78.8 KB | Display | EMDB validaton report |
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Full document | emd_20197_full_validation.pdf.gz | 77.9 KB | Display | |
Data in XML | emd_20197_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20197 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20197 | 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_20197.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.7 Houston strain 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/GI.7/TCH-060/USA/2003
Entire | Name: Norovirus Hu/GI.7/TCH-060/USA/2003 |
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Components |
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-Supramolecule #1: Norovirus Hu/GI.7/TCH-060/USA/2003
Supramolecule | Name: Norovirus Hu/GI.7/TCH-060/USA/2003 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1097017 / Sci species name: Norovirus Hu/GI.7/TCH-060/USA/2003 / Sci species strain: GI.7 / 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: 10.45 MDa |
Virus shell | Shell ID: 1 / Name: VP1 / Diameter: 420.0 Å / T number (triangulation number): 3 |
-Macromolecule #1: Human norovirus GI.7 Snow Mountain Virus strain major capsid (VP1...
Macromolecule | Name: Human norovirus GI.7 Snow Mountain Virus strain major capsid (VP1) protein type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Norovirus Hu/GI.7/TCH-060/USA/2003 |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: DGTSGAGQLV PEVNAAEPLP LEPVVGAATA AATAGQVNLI DPWIMNNF V QAPEGEFTIS PNNTPGDILF DLHLGPHLNP FLQHLSQMYN GWVGNMRVRV MLAGNAFTA GKIIICCVPP GFASQNISIG QATMFPHVIA DVRVLEPIEI PLDDVRNVLF HTNENRPTMR ...String: DGTSGAGQLV PEVNAAEPLP LEPVVGAATA AATAGQVNLI DPWIMNNF V QAPEGEFTIS PNNTPGDILF DLHLGPHLNP FLQHLSQMYN GWVGNMRVRV MLAGNAFTA GKIIICCVPP GFASQNISIG QATMFPHVIA DVRVLEPIEI PLDDVRNVLF HTNENRPTMR LLCMLYTPL RAGGASSGTD PFVIAGRVLT CPSPDFNFLF LVPPSVEQKT RQLTVPNIPL N NLANSRVP AMINKMTVST DQNQVVQFQN GRCTLEGQLL GTTPVSASQV ARIRGKVFST AS GKGLNLT ELDGTPYHAF ESPAPLGFPD IGACDWHVST FKVDQNLSGD PMSRLDVKQN APF APHLGS IEFTSDQDPT GDQLGTLAWV SPSTSGARVD PWKIPSYGST VTESTHLAPP IFPP GFGEA IVYFMSDFPI VSGNTAQVPC TLPQEFVSHF VEQQAPVRGE AALLHYVDPD THRNL GEFK LYPDGFITCV PNTGGGPQNL PTNGVFVFSS WVSRYYQLKP VGT |
-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: 1973 / Average exposure time: 7.0 sec. / Average electron dose: 70.0 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: 2.8 µm / Nominal defocus min: 1.4 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 |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Residue range: 230-526 |
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Refinement | Space: REAL / Protocol: AB INITIO MODEL |