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- EMDB-20250: Mouse norovirus complexed with GCDCA -

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Basic information

Entry
Database: EMDB / ID: EMD-20250
TitleMouse norovirus complexed with GCDCA
Map dataMouse norovirus complexed with GCDCA
Sample
  • Virus: Murine adenovirus 1
    • Protein or peptide: Capsid proteinCapsid
  • Ligand: GLYCOCHENODEOXYCHOLIC ACID
Keywordsnorovirus / bile salts / VIRUS
Function / homologyCalicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / virus-mediated perturbation of host defense response / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Capsid protein
Function and homology information
Biological speciesMurine norovirus 1 / Murine adenovirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSmith TJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)1R01-AI141465 United States
CitationJournal: J Virol / Year: 2019
Title: Bile Salts Alter the Mouse Norovirus Capsid Conformation: Possible Implications for Cell Attachment and Immune Evasion.
Authors: Michael B Sherman / Alexis N Williams / Hong Q Smith / Christopher Nelson / Craig B Wilen / Daved H Fremont / Herbert W Virgin / Thomas J Smith /
Abstract: Caliciviruses are single-stranded RNA viruses with 180 copies of capsid protein comprising the T=3 icosahedral capsids. The main capsid feature is a pronounced protruding (P) domain dimer formed by ...Caliciviruses are single-stranded RNA viruses with 180 copies of capsid protein comprising the T=3 icosahedral capsids. The main capsid feature is a pronounced protruding (P) domain dimer formed by adjacent subunits on the icosahedral surface while the shell domain forms a tight icosahedral sphere around the genome. While the P domain in the crystal structure of human Norwalk virus (genotype I.1) was tightly associated with the shell surface, the cryo-electron microscopy (cryo-EM) structures of several members of the family (mouse norovirus [MNV], rabbit hemorrhagic disease virus, and human norovirus genotype II.10) revealed a "floating" P domain that hovers above the shell by nearly 10 to 15 Å in physiological buffers. Since this unusual feature is shared among, and unique to, the , it suggests an important biological role. Recently, we demonstrated that bile salts enhance cell attachment to the target cell and increase the intrinsic affinity between the P domain and receptor. Presented here are the cryo-EM structures of MNV-1 in the presence of bile salts (∼3 Å) and the receptor CD300lf (∼8 Å). Surprisingly, bile salts cause the rotation and contraction of the P domain onto the shell surface. This both stabilizes the P domain and appears to allow for a higher degree of saturation of receptor onto the virus. Together, these results suggest that, as the virus moves into the gut and the associated high concentrations of bile, the entire capsid face undergoes a conformational change to optimize receptor avidity while the P domain itself undergoes smaller conformational changes to improve receptor affinity. Mouse norovirus and several other members of the have been shown to have a highly unusual structure with the receptor binding protruding (P) domain only loosely tethered to the main capsid shell. Recent studies demonstrated that bile salts enhance the intrinsic P domain/receptor affinity and is necessary for cell attachment. Presented here are the high-resolution cryo-EM structures of apo MNV, MNV/bile salt, and MNV/bile salt/receptor. Bile salts cause a 90° rotation and collapse of the P domain onto the shell surface that may increase the number of available receptor binding sites. Therefore, bile salts appear to be having several effects on MNV. Bile salts shift the structural equilibrium of the P domain toward a form that binds the receptor and away from one that binds antibody. They may also cause the entire P domain to optimize receptor binding while burying a number of potential epitopes.
History
DepositionMay 27, 2019-
Header (metadata) releaseAug 7, 2019-
Map releaseAug 7, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6p4j
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6p4j
  • Imaged by Jmol
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20250.png

Downloads & links

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Map

FileDownload / File: emd_20250.map.gz / Format: CCP4 / Size: 634.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMouse norovirus complexed with GCDCA
Voxel sizeX=Y=Z: 1.1564 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-4.06759 - 8.340144
Average (Standard dev.)0.016859043 (±0.33242983)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-275-275-275
Dimensions550550550
Spacing550550550
CellA=B=C: 636.01996 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.15641.15641.1564
M x/y/z550550550
origin x/y/z0.0000.0000.000
length x/y/z636.020636.020636.020
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ1128100
MAP C/R/S123
start NC/NR/NS-275-275-275
NC/NR/NS550550550
D min/max/mean-4.0688.3400.017

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Supplemental data

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Sample components

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Entire : Murine adenovirus 1

EntireName: Murine adenovirus 1
Components
  • Virus: Murine adenovirus 1
    • Protein or peptide: Capsid proteinCapsid
  • Ligand: GLYCOCHENODEOXYCHOLIC ACID

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Supramolecule #1: Murine adenovirus 1

SupramoleculeName: Murine adenovirus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 10530 / Sci species name: Murine adenovirus 1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Murine norovirus 1
Molecular weightTheoretical: 56.12259 KDa
SequenceString: SGQDLVPAAV EQAVPIQPVA GAALAAPAAG QINQIDPWIF QNFVQCPLGE FSISPRNTPG EILFDLALGP GLNPYLAHLS AMYTGWVGN MEVQLVLAGN AFTAGKVVVA LVPPYFPKGS LTTAQITCFP HVMCDVRTLE PIQLPLLDVR RVLWHATQDQ E ESMRLVCM ...String:
SGQDLVPAAV EQAVPIQPVA GAALAAPAAG QINQIDPWIF QNFVQCPLGE FSISPRNTPG EILFDLALGP GLNPYLAHLS AMYTGWVGN MEVQLVLAGN AFTAGKVVVA LVPPYFPKGS LTTAQITCFP HVMCDVRTLE PIQLPLLDVR RVLWHATQDQ E ESMRLVCM LYTPLRTNSP GDESFVVSGR LLSKPAADFN FVYLTPPIER TIYRMVDLPV IQPRLCTHAR WPAPVYGLLV DP SLPSNPQ WQNGRVHVDG TLLGTTPISG SWVSCFAAEA AYEFQSGTGE VATFTLIEQD GSAYVPGDRA APLGYPDFSG QLE IEVQTE TTKTGDKLKV TTFEMILGPT TNADQAPYQG RVFASVTAAA SLDLVDGRVR AVPRSIYGFQ DTIPEYNDGL LVPL APPIG PFLPGEVLLR FRTYMRQIDT ADAAAEAIDC ALPQEFVSWF ASNAFTVQSE ALLLRYRNTL TGQLLFECKL YNEGY IALS YSGSGPLTFP TDGIFEVVSW VPRLYQLASV GS

UniProtKB: Capsid protein

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Macromolecule #2: GLYCOCHENODEOXYCHOLIC ACID

MacromoleculeName: GLYCOCHENODEOXYCHOLIC ACID / type: ligand / ID: 2 / Number of copies: 6 / Formula: CHO
Molecular weightTheoretical: 449.623 Da
Chemical component information

ChemComp-CHO:
GLYCOCHENODEOXYCHOLIC ACID / detergent*YM / Glycochenodeoxycholic acid

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: OTHER / Average electron dose: 38.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 28463

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