+Open data
-Basic information
Entry | Database: PDB / ID: 7z51 | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Tick-borne encephalitis virus Kuutsalo-14 | ||||||||||||||||||||||||||||||
Components |
| ||||||||||||||||||||||||||||||
Keywords | VIRUS / virion / membrane protein / glycoprotein | ||||||||||||||||||||||||||||||
Function / homology | Function and homology information flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||||||||||||||||||||||||||
Biological species | Tick-borne encephalitis virus | ||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||||||||||||||||||||
Authors | Pulkkinen, L.I.A. / Barrass, S.V. / Anastasina, M. / Butcher, S.J. | ||||||||||||||||||||||||||||||
Funding support | Finland, European Union, Sweden, 9items
| ||||||||||||||||||||||||||||||
Citation | Journal: Viruses / Year: 2022 Title: Molecular Organisation of Tick-Borne Encephalitis Virus. Authors: Lauri I A Pulkkinen / Sarah V Barrass / Aušra Domanska / Anna K Överby / Maria Anastasina / Sarah J Butcher / Abstract: Tick-borne encephalitis virus (TBEV) is a pathogenic, enveloped, positive-stranded RNA virus in the family . Structural studies of flavivirus virions have primarily focused on mosquito-borne species, ...Tick-borne encephalitis virus (TBEV) is a pathogenic, enveloped, positive-stranded RNA virus in the family . Structural studies of flavivirus virions have primarily focused on mosquito-borne species, with only one cryo-electron microscopy (cryo-EM) structure of a tick-borne species published. Here, we present a 3.3 Å cryo-EM structure of the TBEV virion of the Kuutsalo-14 isolate, confirming the overall organisation of the virus. We observe conformational switching of the peripheral and transmembrane helices of M protein, which can explain the quasi-equivalent packing of the viral proteins and highlights their importance in stabilising membrane protein arrangement in the virion. The residues responsible for M protein interactions are highly conserved in TBEV but not in the structurally studied Hypr strain, nor in mosquito-borne flaviviruses. These interactions may compensate for the lower number of hydrogen bonds between E proteins in TBEV compared to the mosquito-borne flaviviruses. The structure reveals two lipids bound in the E protein which are important for virus assembly. The lipid pockets are comparable to those recently described in mosquito-borne Zika, Spondweni, Dengue, and Usutu viruses. Our results thus advance the understanding of tick-borne flavivirus architecture and virion-stabilising interactions. | ||||||||||||||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7z51.cif.gz | 292.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7z51.ent.gz | 248.3 KB | Display | PDB format |
PDBx/mmJSON format | 7z51.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z51_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7z51_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7z51_validation.xml.gz | 69.7 KB | Display | |
Data in CIF | 7z51_validation.cif.gz | 97 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/7z51 ftp://data.pdbj.org/pub/pdb/validation_reports/z5/7z51 | HTTPS FTP |
-Related structure data
Related structure data | 14512MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
EM raw data | EMPIAR-11014 (Title: Single-particle reconstruction of Tick-borne encephalitis virus (Final reconstruction) Data size: 16.4 TB Data #1: Preparation 2 unaligned movies [micrographs - multiframe] Data #2: Preparation 3 unaligned movies [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
| x 60
2 |
|
3 |
| x 5
4 |
| x 6
-Components
#1: Protein | Mass: 53558.270 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tick-borne encephalitis virus (WESTERN SUBTYPE) Strain: Neudoerfl / Cell line: SK-N-SH / Production host: Homo sapiens (human) / References: UniProt: P14336 #2: Protein | Mass: 8311.854 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tick-borne encephalitis virus (WESTERN SUBTYPE) Strain: Neudoerfl / Cell line: SK-N-SH / Production host: Homo sapiens (human) / References: UniProt: P14336 #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Chemical | ChemComp-CPL / Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Tick-borne encephalitis virus / Type: VIRUS Details: Virus was produced in SK-N-SH cells, purified, and inactivated with UV-C. Entity ID: #1-#2 / Source: NATURAL |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: Tick-borne encephalitis virus / Strain: Neudoerfl |
Details of virus | Empty: NO / Enveloped: YES / Isolate: SPECIES / Type: VIRION |
Natural host | Organism: Homo sapiens |
Buffer solution | pH: 8.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2700 nm / Nominal defocus min: 700 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
---|---|
Particle selection | Num. of particles selected: 642026 |
Symmetry | Point symmetry: I (icosahedral) |
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119210 / Symmetry type: POINT |