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- EMDB-47839: MNV Allosteric escape mutant V339I + GCDCA -

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Basic information

Entry
Database: EMDB / ID: EMD-47839
TitleMNV Allosteric escape mutant V339I + GCDCA
Map dataMNV1 Allosteric Escape mutant V339I GCDCA
Sample
  • Virus: Murine norovirus 1
    • Protein or peptide: Capsid protein VP1
  • Ligand: GLYCOCHENODEOXYCHOLIC ACID
Keywordsnorovirus / escape / allosteric / mutant / VIRUS
Function / homologyCalicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / virion component / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / host cell cytoplasm / Capsid protein VP1
Function and homology information
Biological speciesMurine norovirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsSmith TJ / Sherman M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)NIH 1R01-AI141465 United States
CitationJournal: To Be Published
Title: Murine norovirus allosteric escape mutants mimic gut activation.
Authors: Smith TJ
History
DepositionNov 11, 2024-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateMay 7, 2025-
Current statusMay 7, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47839.png

Downloads & links

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Map

FileDownload / File: emd_47839.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMNV1 Allosteric Escape mutant V339I GCDCA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 540 pix.
= 594. Å		1.1 Å/pix.
x 540 pix.
= 594. Å		1.1 Å/pix.
x 540 pix.
= 594. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-2.793528 - 4.1089864
Average (Standard dev.)0.0039499677 (±0.16010399)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 594.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: MNV1 Allosteric Escape mutant V339I GCDCA

Fileemd_47839_half_map_1.map
AnnotationMNV1 Allosteric Escape mutant V339I GCDCA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: MNV1 Allosteric Escape mutant V339I GCDCA

Fileemd_47839_half_map_2.map
AnnotationMNV1 Allosteric Escape mutant V339I GCDCA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Murine norovirus 1

EntireName: Murine norovirus 1
Components
  • Virus: Murine norovirus 1
    • Protein or peptide: Capsid protein VP1
  • Ligand: GLYCOCHENODEOXYCHOLIC ACID

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Supramolecule #1: Murine norovirus 1

SupramoleculeName: Murine norovirus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 223997 / Sci species name: Murine norovirus 1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Murine norovirus 1
Molecular weightTheoretical: 58.583434 KDa
SequenceString: RMSDGAAPKA NGSEASGQDL VPAAVEQAVP IQPVAGAALA APAAGQINQI DPWIFQNFVQ CPLGEFSISP RNTPGEILFD LALGPGLNP YLAHLSAMYT GWVGNMEVQL VLAGNAFTAG KVVVALVPPY FPKGSLTTAQ ITCFPHVMCD VRTLEPIQLP L LDVRRVLW ...String:
RMSDGAAPKA NGSEASGQDL VPAAVEQAVP IQPVAGAALA APAAGQINQI DPWIFQNFVQ CPLGEFSISP RNTPGEILFD LALGPGLNP YLAHLSAMYT GWVGNMEVQL VLAGNAFTAG KVVVALVPPY FPKGSLTTAQ ITCFPHVMCD VRTLEPIQLP L LDVRRVLW HATQDQEESM RLVCMLYTPL RTNSPGDESF VVSGRLLSKP AADFNFVYLT PPIERTIYRM VDLPVIQPRL CT HARWPAP VYGLLVDPSL PSNPQWQNGR VHVDGTLLGT TPISGSWVSC FAAEAAYEFQ SGTGEVATFT LIEQDGSAYV PGD RAAPLG YPDFSGQLEI EIQTETTKTG DKLKVTTFEM ILGPTTNADQ APYQGRVFAS VTAAASLDLV DGRVRAVPRS IYGF QDTIP EYNDGLLVPL APPIGPFLPG EVLLRFRTYM RQIDTADAAA EAIDCALPQE FVSWFASNAF TVQSEALLLR YRNTL TGQL LFECKLYNEG YIALSYSGSG PLTFPTDGIF EVVSWVPRLY QLASVGSLAT GRMLKQ

UniProtKB: Capsid protein VP1

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Macromolecule #2: GLYCOCHENODEOXYCHOLIC ACID

MacromoleculeName: GLYCOCHENODEOXYCHOLIC ACID / type: ligand / ID: 2 / Number of copies: 3 / Formula: CHO
Molecular weightTheoretical: 449.623 Da
Chemical component information

ChemComp-CHO:
GLYCOCHENODEOXYCHOLIC ACID / detergent*YM

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 209918
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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