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- EMDB-20206: Symmetric reconstruction of human norovirus GII.4 Minerva strain ... -

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Entry
Database: EMDB / ID: EMD-20206
TitleSymmetric reconstruction of human norovirus GII.4 Minerva strain VLP in T=4 symmetry
Map dataSymmetric reconstruction of human norovirus GII.4 Minerva strain VLP in T=4 symmetry
Sample
  • Virus: Norovirus Hu/GII.4/Minerva/2006/USA
    • Protein or peptide: Major capsid protein
KeywordsCaliciviridae / Calicivirus / Norovirus / GII.4 / VIRUS LIKE PARTICLE
Function / homologyCalicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Major capsid protein
Function and homology information
Biological speciesNorovirus Hu/GII.4/Minerva/2006/USA
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsJung J / Grant T
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
Title: High-resolution cryo-EM structures of outbreak strain human norovirus shells reveal size variations.
Authors: James Jung / Timothy Grant / Dennis R Thomas / Chris W Diehnelt / Nikolaus Grigorieff / Leemor Joshua-Tor /
Abstract: Noroviruses are a leading cause of foodborne illnesses worldwide. Although GII.4 strains have been responsible for most norovirus outbreaks, the assembled virus shell structures have been available ...Noroviruses are a leading cause of foodborne illnesses worldwide. Although GII.4 strains have been responsible for most norovirus outbreaks, the assembled virus shell structures have been available in detail for only a single strain (GI.1). We present high-resolution (2.6- to 4.1-Å) cryoelectron microscopy (cryo-EM) structures of GII.4, GII.2, GI.7, and GI.1 human norovirus outbreak strain virus-like particles (VLPs). Although norovirus VLPs have been thought to exist in a single-sized assembly, our structures reveal polymorphism between and within genogroups, with small, medium, and large particle sizes observed. Using asymmetric reconstruction, we were able to resolve a Zn metal ion adjacent to the coreceptor binding site, which affected the structural stability of the shell. Our structures serve as valuable templates for facilitating vaccine formulations.
History
DepositionMay 5, 2019-
Header (metadata) releaseMay 29, 2019-
Map releaseJun 26, 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: 0.18
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.18
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ouu
  • Surface level: 0.18
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ouu
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20206.png

Downloads & links

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Map

FileDownload / File: emd_20206.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSymmetric reconstruction of human norovirus GII.4 Minerva strain VLP in T=4 symmetry
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.18 / Movie #1: 0.18
Minimum - Maximum-0.5386191 - 0.8902737
Average (Standard dev.)0.0015412356 (±0.036779247)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 856.00006 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z800800800
origin x/y/z0.0000.0000.000
length x/y/z856.000856.000856.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS800800800
D min/max/mean-0.5390.8900.002

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Supplemental data

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Sample components

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Entire : Norovirus Hu/GII.4/Minerva/2006/USA

EntireName: Norovirus Hu/GII.4/Minerva/2006/USA
Components
  • Virus: Norovirus Hu/GII.4/Minerva/2006/USA
    • Protein or peptide: Major capsid protein

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Supramolecule #1: Norovirus Hu/GII.4/Minerva/2006/USA

SupramoleculeName: Norovirus Hu/GII.4/Minerva/2006/USA / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1182144 / Sci species name: Norovirus Hu/GII.4/Minerva/2006/USA / Sci species strain: GII.4 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.16 MDa
Virus shellShell ID: 1 / Name: VP1 / Diameter: 490.0 Å / T number (triangulation number): 4

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Norovirus Hu/GII.4/Minerva/2006/USA
Molecular weightTheoretical: 58.938098 KDa
Recombinant expressionOrganism: Nicotiana (plant)
SequenceString: MKMASNDANP SDGSAANLVP EVNNEVMALE PVVGAAIAAP VAGQQNVIDP WIRNNFVQAP GGEFTVSPRN APGEILWSAP LGPDLNPYL SHLARMYNGY AGGFEVQVIL AGNAFTAGKI IFAAVPPNFP TEGLSPSQVT MFPHIIVDVR QLEPVLIPLP D VRNNFYHY ...String:
MKMASNDANP SDGSAANLVP EVNNEVMALE PVVGAAIAAP VAGQQNVIDP WIRNNFVQAP GGEFTVSPRN APGEILWSAP LGPDLNPYL SHLARMYNGY AGGFEVQVIL AGNAFTAGKI IFAAVPPNFP TEGLSPSQVT MFPHIIVDVR QLEPVLIPLP D VRNNFYHY NQSNDSTIKL IAMLYTPLRA NNAGEDVFTV SCRVLTRPSP DFDFIFLVPP TVESRTKPFT VPILTVEEMT NS RFPIPLE KLFTGPSGAF VVQPQNGRCT TDGVLLGTTQ LSPVNICTFR GDVTHIAGSR NYTMNLASLN WNNYDPTEEI PAP LGTPDF VGKIQGVLTQ TTKGDGSTRG HKATVYTGSA PFTPKLGSVQ FSTDTENDFE THQNTKFTPV GVIQDGSTTH RNEP QQWVL PSYSGRNVHN VHLAPAVAPT FPGEQLLFFR STMPGCSGYP NMDLDCLLPQ EWVQHFYQEA APAQSDVALL RFVNP DTGR VLFECKLHKS GYVTVAHTGQ HDLVIPPNGY FRFDSWVNQF YTLAPMGNGT GGRRAL

UniProtKB: Major capsid protein

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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

Concentration4 mg/mL
BufferpH: 5.75
GridMaterial: COPPER / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Details: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Specialist opticsEnergy filter - Name: GIF Quantum LS
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 2951 / Average exposure time: 7.0 sec. / Average electron dose: 69.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 94501
Startup modelType of model: OTHER / Details: ab inito
Initial angle assignmentType: COMMON LINE / Software - Name: cisTEM (ver. 1.0.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cisTEM (ver. 1.0.0)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.0.0) / Number images used: 17847
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5iyn


Chain - Chain ID: A / Chain - Residue range: 225-529 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6ouu:
Symmetric reconstruction of human norovirus GII.4 Minerva strain VLP in T=4 symmetry

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