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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-10128 | ||||||||||||
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Title | Thermally-stabilised mutant murine norovirus (MNV-1) | ||||||||||||
![]() | EM density map for heat-stable mutant (hs)MNV, filtered by local resolution. | ||||||||||||
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Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
![]() | Snowden JS / Hurdiss DL / Adeyemi OO / Ranson NA / Herod MR / Stonehouse NJ | ||||||||||||
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 | ![]() | 264.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.9 KB 20.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 17.6 KB | Display | ![]() |
Images | ![]() | 202.3 KB | ||
Masks | ![]() | 476.8 MB | ![]() | |
Others | ![]() ![]() ![]() ![]() | 436.1 MB 372.7 MB 375.7 MB 375.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | EM density map for heat-stable mutant (hs)MNV, filtered by local resolution. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
File | ![]() | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Sharpened density map.
File | emd_10128_additional_1.map | ||||||||||||
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Annotation | Sharpened density map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened density map from 3D refinement.
File | emd_10128_additional_2.map | ||||||||||||
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Annotation | Unsharpened density map from 3D refinement. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: First half map from 3D refinement.
File | emd_10128_half_map_1.map | ||||||||||||
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Annotation | First half map from 3D refinement. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Second half map from 3D refinement.
File | emd_10128_half_map_2.map | ||||||||||||
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Annotation | Second half map from 3D refinement. | ||||||||||||
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: ![]() ![]() |
Host system | Organism: ![]() ![]() |
Virus shell | Shell ID: 1 / T number (triangulation number): 3 |
-Macromolecule #1: Heat-stable mutant murine norovirus (MNV-1) VP1
Macromolecule | Name: Heat-stable mutant murine norovirus (MNV-1) VP1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MRMSDGAAPK ANGSEASGQD LVPAAVEQAV PIQPVAGAAL AAPAAGQINQ IDPWIFQNFV QCPLGEFSIS PRNTPGEILF DLALGPGLNP YLAHLSAMYT GWVGNMEVQL VLAGNAFTAG KVVVALVPPY FPKGSLTTAQ ITCFPHVMCD VRTLEPIQLP LLDVRRVLWH ...String: MRMSDGAAPK ANGSEASGQD LVPAAVEQAV PIQPVAGAAL AAPAAGQINQ IDPWIFQNFV QCPLGEFSIS PRNTPGEILF DLALGPGLNP YLAHLSAMYT GWVGNMEVQL VLAGNAFTAG KVVVALVPPY FPKGSLTTAQ ITCFPHVMCD VRTLEPIQLP LLDVRRVLWH ATQDQEESMR LVCMLYTPLR TNSPGDESFV VSGRLLSKPA ADFNFVYLTP PIERTIYRMV DLPVIQPRLC THARWPAPVY GLLVDPSLPS NPQWQNGRVH VDGTLLGTTP ISGSWVSCFA AEAAYEFQSG TGEVATFTLI EQDGSAYVPG DRAAPLGYPD FSGQLEIEVQ TETTKTGDKL KVTTFEMILG PTTNADQAPY QGRVFASVTA AASLDLVDGR VRAVPRSIYG FQDTIPEYND GQLVPLAPPI GPFLPGEVLL RFRTYMRQID TADAAAEAID CALPQEFVSW FASNAFTVQS EALLLRYRNT LTGQLLFECK LYNEGYIALS YSGSGPLTFP TDGIFEVVSW VPRLYQLASV GSLATGRMLK Q |
-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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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: 64.0 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 |