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- EMDB-20201: Symmetric reconstruction of human norovirus GII.2 Snow Mountain V... -

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Basic information

Entry
Database: EMDB / ID: EMD-20201
TitleSymmetric reconstruction of human norovirus GII.2 Snow Mountain Virus Strain VLP in T=1 symmetry
Map dataSymmetric reconstruction of human norovirus GII.2 Snow Mountain Virus strain VLP in T=1 symmetry
Sample
  • Virus: Snow Mountain virus
    • Protein or peptide: Human norovirus GII.2 Snow Mountain Virus strain major capsid (VP1) protein
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: 2.7 Å
AuthorsJung J / Grant T / Thomas DR / Diehnelt CW / Grigorieff N / Joshua-Tor L
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 4, 2019-
Header (metadata) releaseMay 29, 2019-
Map releaseJun 26, 2019-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.13
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.13
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20201.png

Downloads & links

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Map

FileDownload / File: emd_20201.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSymmetric reconstruction of human norovirus GII.2 Snow Mountain Virus strain VLP in T=1 symmetry
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.13 / Movie #1: 0.13
Minimum - Maximum-0.56177723 - 0.95233476
Average (Standard dev.)0.017774094 (±0.035876352)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 535.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z535.000535.000535.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-0.5620.9520.018

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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: Human norovirus GII.2 Snow Mountain Virus strain major capsid (VP1) protein

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Supramolecule #1: Snow Mountain virus

SupramoleculeName: Snow Mountain virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / 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)
Host systemOrganism: Nicotiana (plant)
Molecular weightExperimental: 3.56 MDa
Virus shellShell ID: 1 / Name: VP1 / Diameter: 310.0 Å / T number (triangulation number): 1

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Macromolecule #1: Human norovirus GII.2 Snow Mountain Virus strain major capsid (VP...

MacromoleculeName: Human norovirus GII.2 Snow Mountain Virus strain major capsid (VP1) protein
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Snow Mountain virus
Recombinant expressionOrganism: Nicotiana (plant)
SequenceString: IIDPWIRANF VQAPNGEFTV SPRNAPGEVL LNLELGPELN PYLAHLARMY NGYAGGMEV QVMLAGNAFT AGKLVFAAVP PHFPVENLSP QQITMFPHVI IDVRTLEPVL LPLPDVRNNF FHYNQKDDPK MRIVAMLYTP LRSNGSGDD VFTVSCRVLT RPSPDFDFTY ...String:
IIDPWIRANF VQAPNGEFTV SPRNAPGEVL LNLELGPELN PYLAHLARMY NGYAGGMEV QVMLAGNAFT AGKLVFAAVP PHFPVENLSP QQITMFPHVI IDVRTLEPVL LPLPDVRNNF FHYNQKDDPK MRIVAMLYTP LRSNGSGDD VFTVSCRVLT RPSPDFDFTY LVPPTVESKT KPFTLPILTL GELSNSRFPV SIDQMYTSPN EVISVQCQNG R CTLDGELQ GTTQLQVSGI CAFKGEVTAH LQDNDHLYNI TITNLNGSPF DPSEDIPAPL GVPDFQGRVF GVITQRDKQN AA GQSQPAN RGHDAVVPTY TAQYTPKLGQ VQIGTWQTDD LKVNQPVKFT PVGLNDTEHF NQWVVPRYAG ALNLNTNLAP SVA PVFPGE RLLFFRSYLP LKGGYGNPAI DCLLPQEWVQ HFYQEAAPSM SEVALVRYIN PDTGRALFEA KLHRAGFMTV SSNT SAPVV VPANGYFRFD SWVNQFYSLA PMG

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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: 1.2 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: 2809 / 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: 76405
CTF correctionSoftware - Name: cisTEM (ver. 1.0.0)
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: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.0.0) / Number images used: 24768
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
RefinementSpace: REAL / Protocol: AB INITIO MODEL

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