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Yorodumi- EMDB-20198: Asymmetric focused reconstruction of human norovirus GI.7 Houston... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20198 | |||||||||
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Title | Asymmetric focused reconstruction of human norovirus GI.7 Houston strain VLP asymmetric unit in T=3 symmetry | |||||||||
Map data | Asymmetric focused reconstruction of human norovirus GI.7 Houston strain VLP asymmetric unit in T=3 symmetry | |||||||||
Sample |
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Keywords | Caliciviridae / Calicivirus / Norovirus / GI.7 / VIRUS LIKE PARTICLE | |||||||||
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: 3.2 Å | |||||||||
Authors | Jung J / Grant T | |||||||||
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_20198.map.gz | 1 MB | EMDB map data format | |
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Header (meta data) | emd-20198-v30.xml emd-20198.xml | 15.8 KB 15.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20198_fsc.xml | 9.8 KB | Display | FSC data file |
Images | emd_20198.png | 150.6 KB | ||
Filedesc metadata | emd-20198.cif.gz | 6.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20198 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20198 | HTTPS FTP |
-Related structure data
Related structure data | 6ou9MC 6otfC 6oucC 6outC 6ouuC 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_20198.map.gz / Format: CCP4 / Size: 4.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Asymmetric focused reconstruction of human norovirus GI.7 Houston strain VLP asymmetric unit 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) |
Molecular weight | Theoretical: 10.45 MDa |
Virus shell | Shell ID: 1 / Name: VP1 / Diameter: 420.0 Å / T number (triangulation number): 3 |
-Macromolecule #1: Major capsid protein
Macromolecule | Name: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Norovirus Hu/GI.7/TCH-060/USA/2003 |
Molecular weight | Theoretical: 58.10073 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MMMASKDAPS NMDGTSGAGQ LVPEVNAAEP LPLEPVVGAA TAAATAGQVN LIDPWIMNNF VQAPEGEFTI SPNNTPGDIL FDLHLGPHL NPFLQHLSQM YNGWVGNMRV RVMLAGNAFT AGKIIICCVP PGFASQNISI GQATMFPHVI ADVRVLEPIE I PLDDVRNV ...String: MMMASKDAPS NMDGTSGAGQ LVPEVNAAEP LPLEPVVGAA TAAATAGQVN LIDPWIMNNF VQAPEGEFTI SPNNTPGDIL FDLHLGPHL NPFLQHLSQM YNGWVGNMRV RVMLAGNAFT AGKIIICCVP PGFASQNISI GQATMFPHVI ADVRVLEPIE I PLDDVRNV LFHTNENRPT MRLLCMLYTP LRAGGASSGT DPFVIAGRVL TCPSPDFNFL FLVPPSVEQK TRQLTVPNIP LN NLANSRV PAMINKMTVS TDQNQVVQFQ NGRCTLEGQL LGTTPVSASQ VARIRGKVFS TASGKGLNLT ELDGTPYHAF ESP APLGFP DIGACDWHVS TFKVDQNLSG DPMSRLDVKQ NAPFAPHLGS IEFTSDQDPT GDQLGTLAWV SPSTSGARVD PWKI PSYGS TVTESTHLAP PIFPPGFGEA IVYFMSDFPI VSGNTAQVPC TLPQEFVSHF VEQQAPVRGE AALLHYVDPD THRNL GEFK LYPDGFITCV PNTGGGPQNL PTNGVFVFSS WVSRYYQLKP VGTAGPARRL GVRRV UniProtKB: Major capsid protein |
-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 / 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: 2.8000000000000003 µm / Nominal defocus min: 1.4000000000000001 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: 225-532 / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: AB INITIO MODEL |
Output model | PDB-6ou9: |