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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-10103 | ||||||||||||
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Title | Cryo-EM structure of murine norovirus (MNV-1) | ||||||||||||
![]() | None | ||||||||||||
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![]() | Norovirus / Virus / Capsid / VP1 | ||||||||||||
Function / homology | Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / virus-mediated perturbation of host defense response / Capsid protein![]() | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
![]() | Snowden JS / Hurdiss DL | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Dynamics in the murine norovirus capsid revealed by high-resolution cryo-EM. Authors: Joseph S Snowden / Daniel L Hurdiss / Oluwapelumi O Adeyemi / Neil A Ranson / Morgan R Herod / Nicola J Stonehouse / ![]() Abstract: Icosahedral viral capsids must undergo conformational rearrangements to coordinate essential processes during the viral life cycle. Capturing such conformational flexibility has been technically ...Icosahedral viral capsids must undergo conformational rearrangements to coordinate essential processes during the viral life cycle. Capturing such conformational flexibility has been technically challenging yet could be key for developing rational therapeutic agents to combat infections. Noroviruses are nonenveloped, icosahedral viruses of global importance to human health. They are a common cause of acute gastroenteritis, yet no vaccines or specific antiviral agents are available. Here, we use genetics and cryo-electron microscopy (cryo-EM) to study the high-resolution solution structures of murine norovirus as a model for human viruses. By comparing our 3 structures (at 2.9- to 3.1-Å resolution), we show that whilst there is little change to the shell domain of the capsid, the radiating protruding domains are flexible, adopting distinct states both independently and synchronously. In doing so, the capsids sample a range of conformational space, with implications for maintaining virion stability and infectivity. | ||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 261.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.4 KB 16.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 17.7 KB | Display | ![]() |
Images | ![]() | 198.3 KB | ||
Masks | ![]() | 476.8 MB | ![]() | |
Filedesc metadata | ![]() | 5.6 KB | ||
Others | ![]() ![]() | 376.7 MB 376.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1015.2 KB | Display | ![]() |
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Full document | ![]() | 1014.7 KB | Display | |
Data in XML | ![]() | 25.5 KB | Display | |
Data in CIF | ![]() | 34 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6s6lMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.065 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_10103_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_10103_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Murine norovirus 1
Entire | Name: ![]() ![]() |
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Components |
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-Supramolecule #1: Murine norovirus 1
Supramolecule | Name: Murine norovirus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: RAW264.7 cells / NCBI-ID: 223997 / Sci species name: Murine norovirus 1 / Sci species strain: CW1P3 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: ![]() ![]() |
Virus shell | Shell ID: 1 / T number (triangulation number): 3 |
-Macromolecule #1: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 58.700598 KDa |
Sequence | String: MRMSDGAAPK ANGSEASGQD LVPAAVEQAV PIQPVAGAAL AAPAAGQINQ IDPWIFQNFV QCPLGEFSIS PRNTPGEILF DLALGPGLN PYLAHLSAMY TGWVGNMEVQ LVLAGNAFTA GKVVVALVPP YFPKGSLTTA QITCFPHVMC DVRTLEPIQL P LLDVRRVL ...String: MRMSDGAAPK ANGSEASGQD LVPAAVEQAV PIQPVAGAAL AAPAAGQINQ IDPWIFQNFV QCPLGEFSIS PRNTPGEILF DLALGPGLN PYLAHLSAMY TGWVGNMEVQ LVLAGNAFTA GKVVVALVPP YFPKGSLTTA QITCFPHVMC DVRTLEPIQL P LLDVRRVL WHATQDQEES MRLVCMLYTP LRTNSPGDES FVVSGRLLSK PAADFNFVYL TPPIERTIYR MVDLPVIQPR LC THARWPA PVYGLLVDPS LPSNPQWQNG RVHVDGTLLG TTPISGSWVS CFAAEAAYEF QSGTGEVATF TLIEQDGSAY VPG DRAAPL GYPDFSGQLE IEVQTETTKT GDKLKVTTFE MILGPTTNAD QAPYQGRVFA SVTAAASLDL VDGRVRAVPR SIYG FQDTI PEYNDGLLVP LAPPIGPFLP GEVLLRFRTY MRQIDTADAA AEAIDCALPQ EFVSWFASNA FTVQSEALLL RYRNT LTGQ LLFECKLYNE GYIALSYSGS GPLTFPTDGI FEVVSWVPRL YQLASVGSLA TGRMLKQ UniProtKB: Capsid protein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.6 Component:
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Grid | Material: COPPER / Mesh: 400 | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 281 K / Instrument: LEICA EM GP |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 59.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |