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Open data
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Basic information
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Title | Purification of Enterovirus A71, strain 4643, WT capsid | |||||||||
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![]() | enterovirus / thermostability / capsid / VIRUS | |||||||||
Function / homology | ![]() symbiont genome entry into host cell via pore formation in plasma membrane / symbiont-mediated suppression of host gene expression / viral capsid / host cell cytoplasm / symbiont entry into host cell / virion attachment to host cell / structural molecule activity / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 14.0 Å | |||||||||
![]() | Catching A / Capponi S / Andino R | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A tradeoff between enterovirus A71 particle stability and cell entry. Authors: Adam Catching / Ming Te Yeh / Simone Bianco / Sara Capponi / Raul Andino / ![]() Abstract: A central role of viral capsids is to protect the viral genome from the harsh extracellular environment while facilitating initiation of infection when the virus encounters a target cell. Viruses are ...A central role of viral capsids is to protect the viral genome from the harsh extracellular environment while facilitating initiation of infection when the virus encounters a target cell. Viruses are thought to have evolved an optimal equilibrium between particle stability and efficiency of cell entry. In this study, we genetically perturb this equilibrium in a non-enveloped virus, enterovirus A71 to determine its structural basis. We isolate a single-point mutation variant with increased particle thermotolerance and decreased efficiency of cell entry. Using cryo-electron microscopy and molecular dynamics simulations, we determine that the thermostable native particles have acquired an expanded conformation that results in a significant increase in protein dynamics. Examining the intermediate states of the thermostable variant reveals a potential pathway for uncoating. We propose a sequential release of the lipid pocket factor, followed by internal VP4 and ultimately the viral RNA. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 26.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.2 KB 19.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.2 KB | Display | ![]() |
Images | ![]() | 92.1 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Filedesc metadata | ![]() | 6.5 KB | ||
Others | ![]() ![]() | 49.3 MB 49.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8e31MC ![]() 8e2xC ![]() 8e2yC ![]() 8e38C ![]() 8e39C ![]() 8e3aC ![]() 8e3bC ![]() 8e3cC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.44 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: #2
File | emd_27853_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_27853_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Human enterovirus 71
Entire | Name: ![]() ![]() |
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Components |
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-Supramolecule #1: Human enterovirus 71
Supramolecule | Name: Human enterovirus 71 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 39054 / Sci species name: Human enterovirus 71 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: ![]() |
Virus shell | Shell ID: 1 / Name: Capsid / Diameter: 300.0 Å / T number (triangulation number): 1 |
-Macromolecule #1: VP1
Macromolecule | Name: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 25.366764 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: SHSTAETTLD SFFSRAGLVG EIDLPLEGTT NPNGYANWDI DITGYAQMRR KVELFTYMRF DAEFTFVACT PTGQVVPQLL QYMFVPPGA PKPDSRESLA WQTATNPSVF VKLSDPPAQV SVPFMSPASA YQWFYDGYPT FGEHKQEKDL EYGACPNNMM G TFSVRTVG ...String: SHSTAETTLD SFFSRAGLVG EIDLPLEGTT NPNGYANWDI DITGYAQMRR KVELFTYMRF DAEFTFVACT PTGQVVPQLL QYMFVPPGA PKPDSRESLA WQTATNPSVF VKLSDPPAQV SVPFMSPASA YQWFYDGYPT FGEHKQEKDL EYGACPNNMM G TFSVRTVG TSKSKYPLVI RIYMRMKHVR AWIPRPMRNQ NYLFKANPNY AGNFIKPTGA SRTAITT UniProtKB: Genome polyprotein |
-Macromolecule #2: Genome polyprotein
Macromolecule | Name: Genome polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 24.917145 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: LTIGNSTITT QEAANIIVGY GEWPSYCSDT RPDVSVNRFY TLDTKLWEKS SKGWYWKFPD VLTETGVFGQ NAQFHYLYRS GFCIHVQCN ASKFHQGALL VAVLPEYVIG TVAGGTGTED SHPPYKQTQP GADGFELQHP YVLDAGIPIS QLTVCPHQWI N LRTNNCAT ...String: LTIGNSTITT QEAANIIVGY GEWPSYCSDT RPDVSVNRFY TLDTKLWEKS SKGWYWKFPD VLTETGVFGQ NAQFHYLYRS GFCIHVQCN ASKFHQGALL VAVLPEYVIG TVAGGTGTED SHPPYKQTQP GADGFELQHP YVLDAGIPIS QLTVCPHQWI N LRTNNCAT IIVPYINALP FDSALNHCNF GLLVVPISPL DYDQGATPVI PITITLAPMC SEFAGLRQ UniProtKB: Genome polyprotein |
-Macromolecule #3: VP3
Macromolecule | Name: VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 23.453926 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: GFPTELKPGT NQFLTTDDGV SAPILPNFHP TPCIHIPGEV RNLLELCQVE TILEVNNVPT NATSLMERLR FPVSAQAGKG ELCAVFRAD PGRSGPWQST LLGQLCGYYT QWSGSLEVTF MFTGSFMATG KMLIAYTPPG GPLPKDRATA MLGTHVIWDF G LQSSVTLV ...String: GFPTELKPGT NQFLTTDDGV SAPILPNFHP TPCIHIPGEV RNLLELCQVE TILEVNNVPT NATSLMERLR FPVSAQAGKG ELCAVFRAD PGRSGPWQST LLGQLCGYYT QWSGSLEVTF MFTGSFMATG KMLIAYTPPG GPLPKDRATA MLGTHVIWDF G LQSSVTLV IPTTGLVSIW YQTNYVVPIG APNTAYIIAL AAAQKNFTMQ LCKDASDIL UniProtKB: Genome polyprotein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7 |
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 6000 pixel / Digitization - Dimensions - Height: 4000 pixel / Number grids imaged: 1 / Average exposure time: 6.0 sec. / Average electron dose: 64.1 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 45000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |