[English] 日本語
Yorodumi- PDB-9g0b: Rhinovirus A2 uncoating intermediate revealing the natural pocket... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9g0b | ||||||
---|---|---|---|---|---|---|---|
Title | Rhinovirus A2 uncoating intermediate revealing the natural pocket factor (pH 5.8 and 4 degrees Celsius) | ||||||
Components |
| ||||||
Keywords | VIRUS / Uncoating Intermediate / Pocket Factor / Lauric Acid | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / ribonucleoside triphosphate phosphatase activity / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / channel activity / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / ribonucleoside triphosphate phosphatase activity / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / channel activity / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / monoatomic ion transmembrane transport / nucleoside-triphosphate phosphatase / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | rhinovirus A2 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Real-Hohn, A. / Blaas, D. | ||||||
Funding support | Austria, 1items
| ||||||
Citation | Journal: To Be Published Title: Rhinovirus A2 uncoating intermediate revealing the natural pocket factor (pH 5.8 and 4 degrees Celsius) Authors: Real-Hohn, A. / Blaas, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 9g0b.cif.gz | 173.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb9g0b.ent.gz | 134.3 KB | Display | PDB format |
PDBx/mmJSON format | 9g0b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9g0b_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 9g0b_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 9g0b_validation.xml.gz | 43.5 KB | Display | |
Data in CIF | 9g0b_validation.cif.gz | 63.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/9g0b ftp://data.pdbj.org/pub/pdb/validation_reports/g0/9g0b | HTTPS FTP |
-Related structure data
Related structure data | 50930MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
| x 60
-Components
#1: Protein | Mass: 32274.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) rhinovirus A2 / References: UniProt: P04936 |
---|---|
#2: Protein | Mass: 29009.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) rhinovirus A2 / References: UniProt: P04936 |
#3: Protein | Mass: 26107.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) rhinovirus A2 / References: UniProt: P04936 |
#4: Protein | Mass: 7356.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) rhinovirus A2 / References: UniProt: P04936 |
#5: Chemical | ChemComp-DAO / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: rhinovirus A2 / Type: VIRUS / Entity ID: #1-#4 / Source: NATURAL | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Experimental value: NO | |||||||||||||||
Source (natural) | Organism: rhinovirus A2 | |||||||||||||||
Details of virus | Empty: NO / Enveloped: NO / Isolate: SEROTYPE / Type: VIRION | |||||||||||||||
Natural host | Organism: Homo sapiens | |||||||||||||||
Virus shell | Diameter: 310 nm / Triangulation number (T number): 3 | |||||||||||||||
Buffer solution | pH: 5.8 / Details: 0.1 M phosphate buffer, pH 5.8 | |||||||||||||||
Buffer component |
| |||||||||||||||
Specimen | Conc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: The virus sample was purified from HeLa cells, diluted to a final concentration of 1 mg/mL in 100 mM potassium phosphate buffer, pH 5.8, and incubated at four degrees for one hour before the vitrification. | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2 | |||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 293 K |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
---|---|
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 100000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 60 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 246 |
-Processing
EM software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 16372 | ||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9825 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 3VDD Accession code: 3VDD / Source name: PDB / Type: experimental model |