[English] 日本語
Yorodumi- PDB-6ouc: Asymmetric focsued reconstruction of human norovirus GII.2 Snow M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ouc | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Asymmetric focsued reconstruction of human norovirus GII.2 Snow Mountain Virus strain VLP asymmetric unit in T=1 symmetry | |||||||||
Components | Viral protein 1 | |||||||||
Keywords | VIRUS LIKE PARTICLE / Caliciviridae / Norovirus / GII.2 / Snow Mountain Virus | |||||||||
Function / homology | Calicivirus 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 species | Snow Mountain virus | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Jung, J. / Grant, T. / Thomas, D.R. / Diehnelt, C.W. / Grigorieff, N. / Joshua-Tor, L. | |||||||||
Funding support | United States, 1items
| |||||||||
Citation | Journal: 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6ouc.cif.gz | 100.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ouc.ent.gz | 74.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ouc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/6ouc ftp://data.pdbj.org/pub/pdb/validation_reports/ou/6ouc | HTTPS FTP |
---|
-Related structure data
Related structure data | 20202MC 6otfC 6ou9C 6outC 6ouuC C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 59321.809 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Snow Mountain virus / Gene: ORF2 / Production host: Nicotiana (plant) / References: UniProt: Q80RD6 |
---|---|
#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Snow Mountain virus / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 3.56 MDa / Experimental value: YES |
Source (natural) | Organism: Snow Mountain virus / Strain: GII.2 |
Source (recombinant) | Organism: Nicotiana (plant) |
Details of virus | Empty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE |
Natural host | Organism: Homo sapiens |
Virus shell | Name: VP1 / Diameter: 310 nm / Triangulation number (T number): 1 |
Buffer solution | pH: 5.75 |
Specimen | Conc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified / Grid material: COPPER |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 295 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 7 sec. / Electron dose: 69 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 2809 |
EM imaging optics | Energyfilter name: GIF Quantum LS |
Image scans | Movie frames/image: 35 |
-Processing
EM software |
| ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 76405 | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1486080 / Algorithm: FOURIER SPACE 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 Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 4RPB Pdb chain-ID: A / Accession code: 4RPB / Pdb chain residue range: 225-532 / Source name: PDB / Type: experimental model |