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- EMDB-7564: Mouse norovirus model using the crystal structure of MNV P domain... -

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Basic information

Entry
Database: EMDB / ID: EMD-7564
TitleMouse norovirus model using the crystal structure of MNV P domain and the Norwalkvirus shell domain
Map datamouse norovirus (MNV-1) in PBS, pH 7.2
Samplemouse norovirus model != Murine norovirus 1

mouse norovirus model

  • Virus: Murine norovirus 1
    • Protein or peptide: Norwalk virus, MNV-1 capsid protein chimera
Keywordsnorovirus / mouse / VIRUS
Function / homology
Function and homology information


antigenic variation / symbiont-mediated perturbation of host defense response / T=3 icosahedral viral capsid / virion component / host cell cytoplasm / identical protein binding
Similarity search - Function
Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Capsid protein VP1 / Capsid protein VP1
Similarity search - Component
Biological speciesMurine norovirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 8.0 Å
AuthorsSmith TJ
CitationJournal: J Virol / Year: 2010
Title: High-resolution cryo-electron microscopy structures of murine norovirus 1 and rabbit hemorrhagic disease virus reveal marked flexibility in the receptor binding domains.
Authors: Umesh Katpally / Neil R Voss / Tommaso Cavazza / Stefan Taube / John R Rubin / Vivienne L Young / Jeanne Stuckey / Vernon K Ward / Herbert W Virgin / Christiane E Wobus / Thomas J Smith /
Abstract: Our previous structural studies on intact, infectious murine norovirus 1 (MNV-1) virions demonstrated that the receptor binding protruding (P) domains are lifted off the inner shell of the virus. ...Our previous structural studies on intact, infectious murine norovirus 1 (MNV-1) virions demonstrated that the receptor binding protruding (P) domains are lifted off the inner shell of the virus. Here, the three-dimensional (3D) reconstructions of recombinant rabbit hemorrhagic disease virus (rRHDV) virus-like particles (VLPs) and intact MNV-1 were determined to approximately 8-A resolution. rRHDV also has a raised P domain, and therefore, this conformation is independent of infectivity and genus. The atomic structure of the MNV-1 P domain was used to interpret the MNV-1 reconstruction. Connections between the P and shell domains and between the floating P domains were modeled. This observed P-domain flexibility likely facilitates virus-host receptor interactions.
History
DepositionMar 19, 2018-
Header (metadata) releaseApr 4, 2018-
Map releaseApr 4, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6crj
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6crj
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7564.png

Downloads & links

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Map

FileDownload / File: emd_7564.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmouse norovirus (MNV-1) in PBS, pH 7.2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.56 Å/pix.
x 384 pix.
= 599.002 Å		1.56 Å/pix.
x 384 pix.
= 599.002 Å		1.56 Å/pix.
x 384 pix.
= 599.002 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.5599 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 2.5 / Movie #1: 2
Minimum - Maximum-11.953576 - 14.875709000000001
Average (Standard dev.)-0.000013676187 (±0.9340035)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-192-192-191
Dimensions384384384
Spacing384384384
CellA=B=C: 599.0016 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.55990104166671.55990104166671.5599010416667
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z599.002599.002599.002
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-192-192-191
NC/NR/NS384384384
D min/max/mean-11.95414.876-0.000

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Supplemental data

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Sample components

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Entire : mouse norovirus model

EntireName: mouse norovirus model
Components
  • Virus: Murine norovirus 1
    • Protein or peptide: Norwalk virus, MNV-1 capsid protein chimera

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Supramolecule #1: Murine norovirus 1

SupramoleculeName: Murine norovirus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: chimera of Norwalk virus shell domain and MNV P domain
NCBI-ID: 223997 / Sci species name: Murine norovirus 1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Mus (mice)

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Macromolecule #1: Norwalk virus, MNV-1 capsid protein chimera

MacromoleculeName: Norwalk virus, MNV-1 capsid protein chimera / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Murine norovirus 1
Molecular weightTheoretical: 57.127523 KDa
Recombinant expressionOrganism: Mus abbotti (Abbott's mouse)
SequenceString: SSVDGASGAG QLVPEVNASD PLAMDPVAGS STAVATAGQV NPIDPWIINN FVQAPQGEFT ISPNNTPGDV LFDLSLGPHL NPFLLHLSQ MYNGWVGNMR VRIMLAGNAF TAGKIIVSCI PPGFGSHNLT IAQATLFPHV IADVRTLDPI EVPLEDVRNV L FHNNDRNQ ...String:
SSVDGASGAG QLVPEVNASD PLAMDPVAGS STAVATAGQV NPIDPWIINN FVQAPQGEFT ISPNNTPGDV LFDLSLGPHL NPFLLHLSQ MYNGWVGNMR VRIMLAGNAF TAGKIIVSCI PPGFGSHNLT IAQATLFPHV IADVRTLDPI EVPLEDVRNV L FHNNDRNQ QTMRLVCMLY TPLRTGGGTG DSFVVAGRVM TCPSPDFNFL FLVPAAAAAA RMVDLPVIQP RLCTHARWPA PV YGLLVDP SLPSNPQWQN GRVHVDGTLL GTTPISGSWV SCFAAEAAYE FQSGTGEVAT FTLIEQDGSA YVPGDRAAPL GYP DFSGQL EIEVQTETTK TGDKLKVTTF EMILGPTTNA DQAPYQGRVF ASVTAAASLD LVDGRVRAVP RSIYGFQDTI PEYN DGLLV PLAPPIGPFL PGEVLLRFRT YMRQIDTADA AAEAIDCALP QEFVSWFASN AFTVQSEALL LRYRNTLTGQ LLFEC KLYN EGYIALSYSG SGPLTFPTDG IFEVVSWVPR LYQLASVGSL ATGRMLK

UniProtKB: Capsid protein VP1, Capsid protein VP1

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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 / Details: PBS
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: FEI EAGLE (2k x 2k) / Average electron dose: 10.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 20425
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-6crj:
Mouse norovirus model using the crystal structure of MNV P domain and the Norwalkvirus shell domain

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