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- EMDB-20195: Symmetric reconstruction of human norovirus GII.2 Snow Mountain V... -

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Basic information

Entry
Database: EMDB / ID: EMD-20195
TitleSymmetric reconstruction of human norovirus GII.2 Snow Mountain Virus Strain VLP in T=3 symmetry
Map dataSymmetric reconstruction of human norovirus GII.2 Snow Mountain Virus strain VLP in T=3 symmetry
Sample
  • Virus: Snow Mountain virus
    • Protein or peptide: Viral protein 1
  • Ligand: ZINC ION
KeywordsCaliciviridae / Norovirus / GII.2 / Snow Mountain Virus / 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 / Viral protein 1
Function and homology information
Biological speciesSnow Mountain virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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 3, 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: 0.16
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.16
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6otf
  • Surface level: 0.16
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6otf
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20195.png

Downloads & links

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Map

FileDownload / File: emd_20195.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSymmetric reconstruction of human norovirus GII.2 Snow Mountain Virus strain VLP in T=3 symmetry
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 800 pix.
= 856. Å		1.07 Å/pix.
x 800 pix.
= 856. Å		1.07 Å/pix.
x 800 pix.
= 856. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16 / Movie #1: 0.16
Minimum - Maximum-0.39786363 - 0.7525375
Average (Standard dev.)0.016850358 (±0.037322648)
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
start NX/NY/NZ000
NX/NY/NZ304304304
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS800800800
D min/max/mean-0.3980.7530.017

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Supplemental data

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Sample components

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Entire : Snow Mountain virus

EntireName: Snow Mountain virus
Components
  • Virus: Snow Mountain virus
    • Protein or peptide: Viral protein 1
  • Ligand: ZINC ION

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Supramolecule #1: Snow Mountain virus

SupramoleculeName: Snow Mountain virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 52276 / Sci species name: Snow Mountain virus / Sci species strain: GII.2 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.68 MDa
Virus shellShell ID: 1 / Name: VP1 / Diameter: 430.0 Å / T number (triangulation number): 3

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Macromolecule #1: Viral protein 1

MacromoleculeName: Viral protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Snow Mountain virus
Molecular weightTheoretical: 59.321809 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKMASNDAAP STDGAAGLVP ESNNEVMALE PVAGAALAAP VTGQTNIIDP WIRANFVQAP NGEFTVSPRN APGEVLLNLE LGPELNPYL AHLARMYNGY AGGMEVQVML AGNAFTAGKL VFAAVPPHFP VENLSPQQIT MFPHVIIDVR TLEPVLLPLP D VRNNFFHY ...String:
MKMASNDAAP STDGAAGLVP ESNNEVMALE PVAGAALAAP VTGQTNIIDP WIRANFVQAP NGEFTVSPRN APGEVLLNLE LGPELNPYL AHLARMYNGY AGGMEVQVML AGNAFTAGKL VFAAVPPHFP VENLSPQQIT MFPHVIIDVR TLEPVLLPLP D VRNNFFHY NQKDDPKMRI VAMLYTPLRS NGSGDDVFTV SCRVLTRPSP DFDFTYLVPP TVESKTKPFT LPILTLGELS NS RFPVSID QMYTSPNEVI SVQCQNGRCT LDGELQGTTQ LQVSGICAFK GEVTAHLQDN DHLYNITITN LNGSPFDPSE DIP APLGVP DFQGRVFGVI TQRDKQNAAG QSQPANRGHD AVVPTYTAQY TPKLGQVQIG TWQTDDLKVN QPVKFTPVGL NDTE HFNQW VVPRYAGALN LNTNLAPSVA PVFPGERLLF FRSYLPLKGG YGNPAIDCLL PQEWVQHFYQ EAAPSMSEVA LVRYI NPDT GRALFEAKLH RAGFMTVSSN TSAPVVVPAN GYFRFDSWVN QFYSLAPMGT GNGRRRIQ

UniProtKB: Viral protein 1

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 2809 / Average exposure time: 7.0 sec. / Average electron dose: 69.0 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: 2.6 µm / Nominal defocus min: 1.2 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: 40744
Startup modelType of model: OTHER / Details: ab inito
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.0.0) / Number images used: 1540
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 3D classificationSoftware - Name: cisTEM (ver. 1.0.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4rpb


Chain - Chain ID: A / Chain - Residue range: 225-532 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6otf:
Symmetric reconstruction of human norovirus GII.2 Snow Mountain Virus Strain VLP in T=3 symmetry

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