+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24226 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Mouse norovirus (MNV-1) capsid at pH 7.5 | |||||||||
Map data | Mouse norovirus at pH 7.5 | |||||||||
Sample |
| |||||||||
Keywords | norovirus / mouse / pH 7.5 / VIRUS | |||||||||
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 / metal ion binding / Capsid protein VP1 Function and homology information | |||||||||
Biological species | Murine norovirus 1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Smith TJ | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: J Virol / Year: 2021 Title: Multiple Signals in the Gut Contract the Mouse Norovirus Capsid To Block Antibody Binding While Enhancing Receptor Affinity. Authors: Alexis N Williams / Michael B Sherman / Hong Q Smith / Stefan Taube / B Montgomery Pettitt / Christiane E Wobus / Thomas J Smith / Abstract: Human norovirus is the leading cause of gastroenteritis worldwide, with no approved vaccine or antiviral treatment to mitigate infection. These plus-strand RNA viruses have T = 3 icosahedral ...Human norovirus is the leading cause of gastroenteritis worldwide, with no approved vaccine or antiviral treatment to mitigate infection. These plus-strand RNA viruses have T = 3 icosahedral protein capsids with 90 pronounced protruding (P) domain dimers, to which antibodies and cellular receptors bind. We previously demonstrated that bile binding to the capsid of mouse norovirus (MNV) causes several major conformational changes; the entire P domain rotates by ∼90° and contracts onto the shell, the P domain dimers rotate about each other, and the structural equilibrium of the epitopes at the top of the P domain shifts toward the closed conformation, which favors receptor binding while blocking antibody binding. Here, we demonstrate that MNV undergoes reversible conformational changes at pH 5.0 that are nearly identical to those observed when bile binds. Notably, at low pH or when metals bind, a cluster of acidic resides in the G'-H' loop interact and distort the G'-H' loop, and this may drive C'-D' loop movement toward the closed conformation. Enzyme-linked immunosorbent assays with infectious virus particles at low pH or in the presence of metals demonstrated that all tested antibodies do not bind to this contracted form, akin to what was observed with the MNV-bile complex. Therefore, low pH, cationic metals, and bile salts are physiological triggers in the gut for P domain contraction and structural rearrangement, which synergistically prime the virus for receptor binding while blocking antibody binding. The protruding domains on the calicivirus capsids are recognized by cell receptors and antibodies. We demonstrated that MNV P domains are highly mobile, and bile causes contraction onto the shell surface while allosterically blocking antibody binding. We present the near-atomic cryo-electron microscopy structures of infectious MNV at pH 5.0 and pH 7.5. Surprisingly, low pH is sufficient to cause the same conformational changes as when bile binds. A cluster of acidic residues on the G'-H' loop were most likely involved in the pH effects. These residues also bound divalent cations and had the same conformation as observed here at pH 5. Binding assays demonstrated that low pH and metals block antibody binding, and thus the G'-H' loop might be driving the conformational changes. Therefore, low pH, cationic metals, and bile salts in the gut synergistically prime the virus for receptor binding while blocking antibody binding. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_24226.map.gz | 433.9 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-24226-v30.xml emd-24226.xml | 9.5 KB 9.5 KB | Display Display | EMDB header |
Images | emd_24226.png | 208.4 KB | ||
Filedesc metadata | emd-24226.cif.gz | 5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24226 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24226 | HTTPS FTP |
-Validation report
Summary document | emd_24226_validation.pdf.gz | 521.1 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_24226_full_validation.pdf.gz | 520.7 KB | Display | |
Data in XML | emd_24226_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | emd_24226_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24226 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24226 | HTTPS FTP |
-Related structure data
Related structure data | 7n7fMC 7n6yC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_24226.map.gz / Format: CCP4 / Size: 909.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Mouse norovirus at pH 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0855 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Murine norovirus 1
Entire | Name: Murine norovirus 1 |
---|---|
Components |
|
-Supramolecule #1: Murine norovirus 1
Supramolecule | Name: Murine norovirus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Grown in mouse BV2 cell line / NCBI-ID: 223997 / Sci species name: Murine norovirus 1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
---|
-Macromolecule #1: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Murine norovirus 1 |
Molecular weight | Theoretical: 58.70066 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 CFAAEAAYKF 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 VP1 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Details: 25 mM citrate, 25 mM phosphate, pH 7.5, 100 mM NaCl |
---|---|
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 145347 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |