[English] 日本語
Yorodumi- EMDB-6637: The novel asymmetric entry intermediate of a picornavirus capture... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6637 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The novel asymmetric entry intermediate of a picornavirus captured with nanodiscs | |||||||||
Map data | Icosahedral reconstruction of CVB3 A-particle (sharpened) | |||||||||
Sample |
| |||||||||
Keywords | Picornavirus / entry intermediate | |||||||||
Function / homology | Function and homology information RNA-protein covalent cross-linking / : / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C ...RNA-protein covalent cross-linking / : / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / 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 / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / symbiont-mediated suppression of host gene expression / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / DNA replication / RNA helicase activity / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / nucleus / metal ion binding Similarity search - Function | |||||||||
Biological species | Human coxsackievirus B3 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Lee H / Shingler KL / Organtini LJ / Ashley RE / Makhov AM / Conway JF / Hafenstein S | |||||||||
Citation | Journal: Sci Adv / Year: 2016 Title: The novel asymmetric entry intermediate of a picornavirus captured with nanodiscs. Authors: Hyunwook Lee / Kristin L Shingler / Lindsey J Organtini / Robert E Ashley / Alexander M Makhov / James F Conway / Susan Hafenstein / Abstract: Many nonenveloped viruses engage host receptors that initiate capsid conformational changes necessary for genome release. Structural studies on the mechanisms of picornavirus entry have relied on in ...Many nonenveloped viruses engage host receptors that initiate capsid conformational changes necessary for genome release. Structural studies on the mechanisms of picornavirus entry have relied on in vitro approaches of virus incubated at high temperatures or with excess receptor molecules to trigger the entry intermediate or A-particle. We have induced the coxsackievirus B3 entry intermediate by triggering the virus with full-length receptors embedded in lipid bilayer nanodiscs. These asymmetrically formed A-particles were reconstructed using cryo-electron microscopy and a direct electron detector. These first high-resolution structures of a picornavirus entry intermediate captured at a membrane with and without imposing icosahedral symmetry (3.9 and 7.8 Å, respectively) revealed a novel A-particle that is markedly different from the classical A-particles. The asymmetric receptor binding triggers minimal global capsid expansion but marked local conformational changes at the site of receptor interaction. In addition, viral proteins extrude from the capsid only at the site of extensive protein remodeling adjacent to the nanodisc. Thus, the binding of the receptor triggers formation of a unique site in preparation for genome release. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6637.map.gz | 223.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-6637-v30.xml emd-6637.xml | 10.1 KB 10.1 KB | Display Display | EMDB header |
Images | emd_6637.png | 1.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6637 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6637 | HTTPS FTP |
-Validation report
Summary document | emd_6637_validation.pdf.gz | 361.9 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_6637_full_validation.pdf.gz | 361.4 KB | Display | |
Data in XML | emd_6637_validation.xml.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6637 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6637 | HTTPS FTP |
-Related structure data
Related structure data | 3jd7MC 6636C 6638C C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_6637.map.gz / Format: CCP4 / Size: 238.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Icosahedral reconstruction of CVB3 A-particle (sharpened) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.37 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Locally-stimulated A-particle of CVB3
Entire | Name: Locally-stimulated A-particle of CVB3 |
---|---|
Components |
|
-Supramolecule #1000: Locally-stimulated A-particle of CVB3
Supramolecule | Name: Locally-stimulated A-particle of CVB3 / type: sample / ID: 1000 / Number unique components: 1 |
---|
-Supramolecule #1: Human coxsackievirus B3
Supramolecule | Name: Human coxsackievirus B3 / type: virus / ID: 1 Details: CAR-nanodisc was incubated with the virus sample at 37 degrees Celsius for 30 minutes. NCBI-ID: 12072 / Sci species name: Human coxsackievirus B3 / Sci species strain: 28 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
---|---|
Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
Virus shell | Shell ID: 1 / Name: VP1-4 / Diameter: 300 Å / T number (triangulation number): 1 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.0 mg/mL |
---|---|
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 102 K / Instrument: GATAN CRYOPLUNGE 3 |
-Electron microscopy
Microscope | FEI POLARA 300 |
---|---|
Date | Nov 21, 2014 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 9685 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 5.875 µm / Nominal defocus min: 1.362 µm |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Each particle |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 57203 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: 1 / Chain - #1 - Chain ID: 2 / Chain - #2 - Chain ID: 3 / Chain - #3 - Chain ID: 4 |
---|---|
Software | Name: Phenix |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | PDB-3jd7: |