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- EMDB-20205: Asymmetric focused reconstruction of human norovirus GI.1 Norwalk... -

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Basic information

Entry
Database: EMDB / ID: EMD-20205
TitleAsymmetric focused reconstruction of human norovirus GI.1 Norwalk strain VLP asymmetric unit in T=3 symmetry
Map dataAsymmetric focused reconstruction of human norovirus GI.1 Norwalk strain VLP asymmetric unit in T=3 symmetry
Sample
  • Virus: Norovirus Hu/1968/US
    • Protein or peptide: Capsid protein VP1
  • Ligand: water
KeywordsCaliciviridae / Norovirus / GI.1 / Norwalk / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


T=3 icosahedral viral capsid / 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
Biological speciesNorwalk virus (strain GI/Human/United States/Norwalk/1968) / Norovirus Hu/1968/US
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 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: 0.12
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6out
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20205.png

Downloads & links

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Map

FileDownload / File: emd_20205.map.gz / Format: CCP4 / Size: 4.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAsymmetric focused reconstruction of human norovirus GI.1 Norwalk strain VLP asymmetric unit in T=3 symmetry
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 104 pix.
= 111.28 Å		1.07 Å/pix.
x 112 pix.
= 119.84 Å		1.07 Å/pix.
x 98 pix.
= 104.86 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12 / Movie #1: 0.12
Minimum - Maximum-0.45164528 - 0.71380645
Average (Standard dev.)0.004923987 (±0.059667923)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions11298104
Spacing98112104
CellA: 104.86001 Å / B: 119.840004 Å / C: 111.28001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z98112104
origin x/y/z0.0000.0000.000
length x/y/z104.860119.840111.280
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ304304304
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS98112104
D min/max/mean-0.4520.7140.005

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Supplemental data

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Sample components

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Entire : Norovirus Hu/1968/US

EntireName: Norovirus Hu/1968/US
Components
  • Virus: Norovirus Hu/1968/US
    • Protein or peptide: Capsid protein VP1
  • Ligand: water

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Supramolecule #1: Norovirus Hu/1968/US

SupramoleculeName: Norovirus Hu/1968/US / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 524364 / Sci species name: Norovirus Hu/1968/US / Sci species strain: GI.1 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.19 MDa
Virus shellShell ID: 1 / Name: VP1 / Diameter: 410.0 Å / T number (triangulation number): 3

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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: Norwalk virus (strain GI/Human/United States/Norwalk/1968)
Strain: GI/Human/United States/Norwalk/1968
Molecular weightTheoretical: 56.629828 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MMMASKDATS SVDGASGAGQ LVPEVNASDP LAMDPVAGSS TAVATAGQVN PIDPWIINNF VQAPQGEFTI SPNNTPGDVL FDLSLGPHL NPFLLHLSQM YNGWVGNMRV RIMLAGNAFT AGKIIVSCIP PGFGSHNLTI AQATLFPHVI ADVRTLDPIE V PLEDVRNV ...String:
MMMASKDATS SVDGASGAGQ LVPEVNASDP LAMDPVAGSS TAVATAGQVN PIDPWIINNF VQAPQGEFTI SPNNTPGDVL FDLSLGPHL NPFLLHLSQM YNGWVGNMRV RIMLAGNAFT AGKIIVSCIP PGFGSHNLTI AQATLFPHVI ADVRTLDPIE V PLEDVRNV LFHNNDRNQQ TMRLVCMLYT PLRTGGGTGD SFVVAGRVMT CPSPDFNFLF LVPPTVEQKT RPFTLPNLPL SS LSNSRAP LPISSMGISP DNVQSVQFQN GRCTLDGRLV GTTPVSLSHV AKIRGTSNGT VINLTELDGT PFHPFEGPAP IGF PDLGGC DWHINMTQFG HSSQTQYDVD TTPDTFVPHL GSIQANGIGS GNYVGVLSWI SPPSHPSGSQ VDLWKIPNYG SSIT EATHL APSVYPPGFG EVLVFFMSKM PGPGAYNLPC LLPQEYISHL ASEQAPTVGE AALLHYVDPD TGRNLGEFKA YPDGF LTCV PNGASSGPQQ LPINGVFVFV SWVSRFYQLK PVGTASSARG RLGLRR

UniProtKB: Capsid protein VP1

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 226 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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
Specialist opticsEnergy filter - Name: GIF Quantum LS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 1820 / Average exposure time: 7.0 sec. / Average electron dose: 78.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 38535
Startup modelType of model: OTHER / Details: ab inito
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.0.0)
Details: Symmetry expansion and signal subtraction of the icosahedral asymmetric units from the whole particle images, followed by asymmetric focused reconstruction towards the apex of the spike domain
Number images used: 293580
Initial angle assignmentType: COMMON LINE / Software - Name: cisTEM (ver. 1.0.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cisTEM (ver. 1.0.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

1ihm

chain_id: A, residue_range: 29-520, source_name: PDB, initial_model_type: experimental model

1ihm

chain_id: B, residue_range: 10-520, source_name: PDB, initial_model_type: experimental model

1ihm

chain_id: C, residue_range: 29-520, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6out:
Asymmetric focused reconstruction of human norovirus GI.1 Norwalk strain VLP asymmetric unit in T=3 symmetry

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