[English] 日本語
Yorodumi- EMDB-5519: Electron cryo-tomography of coxsackievirus A9-integrin alpha v be... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5519 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Electron cryo-tomography of coxsackievirus A9-integrin alpha v beta 6 complex | |||||||||
Map data | Electron cryo-tomography of coxsackievirus A9-integrin alpha v beta 6 complex | |||||||||
Sample |
| |||||||||
Keywords | CVA9-integrin / picornavirus / enterovirus / coxsackievirus A9 / integrin / tomography | |||||||||
Biological species | Human coxsackievirus A9 | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Shakeel S / Seitsonen JJT / Kajander T / Laurinmaki P / Hyypia T / Susi P / Butcher SJ | |||||||||
Citation | Journal: J Virol / Year: 2013 Title: Structural and functional analysis of coxsackievirus A9 integrin αvβ6 binding and uncoating. Authors: Shabih Shakeel / Jani J T Seitsonen / Tommi Kajander / Pasi Laurinmäki / Timo Hyypiä / Petri Susi / Sarah J Butcher / Abstract: Coxsackievirus A9 (CVA9) is an important pathogen of the Picornaviridae family. It utilizes cellular receptors from the integrin αv family for binding to its host cells prior to entry and genome ...Coxsackievirus A9 (CVA9) is an important pathogen of the Picornaviridae family. It utilizes cellular receptors from the integrin αv family for binding to its host cells prior to entry and genome release. Among the integrins tested, it has the highest affinity for αvβ6, which recognizes the arginine-glycine-aspartic acid (RGD) loop present on the C terminus of viral capsid protein, VP1. As the atomic model of CVA9 lacks the RGD loop, we used surface plasmon resonance, electron cryo-microscopy, and image reconstruction to characterize the capsid-integrin interactions and the conformational changes on genome release. We show that the integrin binds to the capsid with nanomolar affinity and that the binding of integrin to the virion does not induce uncoating, thereby implying that further steps are required for release of the genome. Electron cryo-tomography and single-particle image reconstruction revealed variation in the number and conformation of the integrins bound to the capsid, with the integrin footprint mapping close to the predicted site for the exposed RGD loop on VP1. Comparison of empty and RNA-filled capsid reconstructions showed that the capsid undergoes conformational changes when the genome is released, so that the RNA-capsid interactions in the N termini of VP1 and VP4 are lost, VP4 is removed, and the capsid becomes more porous, as has been reported for poliovirus 1, human rhinovirus 2, enterovirus 71, and coxsackievirus A7. These results are important for understanding the structural basis of integrin binding to CVA9 and the molecular events leading to CVA9 cell entry and uncoating. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5519.map.gz | 146.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-5519-v30.xml emd-5519.xml | 7.7 KB 7.7 KB | Display Display | EMDB header |
Images | emd_5519_1.jpg | 245.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5519 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5519 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_5519.map.gz / Format: CCP4 / Size: 227.2 MB / Type: IMAGE STORED AS SIGNED BYTE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Electron cryo-tomography of coxsackievirus A9-integrin alpha v beta 6 complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 7.68 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : coxsackievirus A9 in complex with integrin alpha v beta 6
Entire | Name: coxsackievirus A9 in complex with integrin alpha v beta 6 |
---|---|
Components |
|
-Supramolecule #1000: coxsackievirus A9 in complex with integrin alpha v beta 6
Supramolecule | Name: coxsackievirus A9 in complex with integrin alpha v beta 6 type: sample / ID: 1000 / Number unique components: 2 |
---|
-Supramolecule #1: Human coxsackievirus A9
Supramolecule | Name: Human coxsackievirus A9 / type: virus / ID: 1 / Name.synonym: CVA9 Details: 10nm gold particles present in tomogram as fiducial. NCBI-ID: 12067 / Sci species name: Human coxsackievirus A9 / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: CVA9 |
---|---|
Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
Virus shell | Shell ID: 1 / T number (triangulation number): 1 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | electron tomography |
-Sample preparation
Vitrification | Cryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3 |
---|
-Electron microscopy
Microscope | FEI TECNAI F20 |
---|---|
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 39000 |
Sample stage | Specimen holder: GATAN 262 / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° / Tilt series - Axis1 - Angle increment: 3 ° |
Date | Jan 21, 2011 |
Image recording | Category: CCD / Film or detector model: GENERIC CCD |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: OTHER / Software - Name: IMOD / Number images used: 40 |
---|