+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27863 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Purification of Enterovirus A71, strain 4643, WT capsid | |||||||||
Map data | Purification of Enterovirus A71, strain 4643, WT capsid | |||||||||
Sample |
| |||||||||
Keywords | enterovirus / thermostability / capsid / VIRUS | |||||||||
Function / homology | Function and homology information symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 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 / channel activity ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 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 / channel activity / nucleoside-triphosphate phosphatase / monoatomic ion transmembrane transport / 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 / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Enterovirus A71 / Human enterovirus 71 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.1 Å | |||||||||
Authors | Catching A / Capponi S / Andino R | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: Nat Commun / Year: 2023 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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_27863.map.gz | 26.1 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-27863-v30.xml emd-27863.xml | 19.7 KB 19.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27863_fsc.xml | 9.2 KB | Display | FSC data file |
Images | emd_27863.png | 129.3 KB | ||
Masks | emd_27863_msk_1.map | 1.1 MB | Mask map | |
Filedesc metadata | emd-27863.cif.gz | 6.3 KB | ||
Others | emd_27863_half_map_1.map.gz emd_27863_half_map_2.map.gz | 49.5 MB 49.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27863 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27863 | HTTPS FTP |
-Validation report
Summary document | emd_27863_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_27863_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_27863_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | emd_27863_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27863 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27863 | HTTPS FTP |
-Related structure data
Related structure data | 8e3cMC 8e2xC 8e2yC 8e31C 8e38C 8e39C 8e3aC 8e3bC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_27863.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Purification of Enterovirus A71, strain 4643, WT capsid | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.44 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_27863_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Purification of Enterovirus A71, strain 4643, WT capsid
File | emd_27863_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Purification of Enterovirus A71, strain 4643, WT capsid | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Purification of Enterovirus A71, strain 4643, WT capsid
File | emd_27863_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Purification of Enterovirus A71, strain 4643, WT capsid | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Human enterovirus 71
Entire | Name: Human enterovirus 71 |
---|---|
Components |
|
-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 |
---|---|
Host (natural) | Organism: Homo sapiens (human) |
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 / EC number: picornain 2A |
---|---|
Source (natural) | Organism: Enterovirus A71 / Strain: Tainan/4643/98 |
Molecular weight | Theoretical: 25.366697 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: SHSTAETTLD SFFSRAGLVG EIDLPLEGTT NPNGYANWDI DITGYAQMRR KVELFTYMRF DAEFTFVACT PTGQVVPQLL QYMFVPPGA PEPDSRESLA WQTATNPSVF VKLSDPPAQV SVPFMSPASA YQWFYDGYPT FGEHKQEKDL EYGACPNNMM G TFSVRTVG ...String: SHSTAETTLD SFFSRAGLVG EIDLPLEGTT NPNGYANWDI DITGYAQMRR KVELFTYMRF DAEFTFVACT PTGQVVPQLL QYMFVPPGA PEPDSRESLA WQTATNPSVF VKLSDPPAQV SVPFMSPASA YQWFYDGYPT FGEHKQEKDL EYGACPNNMM G TFSVRTVG TSKSKYPLVI RIYMRMKHVR AWIPRPMRNQ NYLFKANPNY AGNFIKPTGA SRTAITT UniProtKB: Genome polyprotein |
-Macromolecule #2: VP2
Macromolecule | Name: VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Enterovirus A71 / Strain: Tainan/4643/98 |
Molecular weight | Theoretical: 25.803088 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: LTIGNSTITT QEAANIIVGY GEWPSYCSDS DATAVDKPTR PDVSVNRFYT LDTKLWEKSS KGWYWKFPDV LTETGVFGQN AQFHYLYRS GFCIHVQCNA SKFHQGALLV AVLPEYVIGT VAGGTGTEDS HPPYKQTQPG ADGFELQHPY VLDAGIPISQ L TVCPHQWI ...String: LTIGNSTITT QEAANIIVGY GEWPSYCSDS DATAVDKPTR PDVSVNRFYT LDTKLWEKSS KGWYWKFPDV LTETGVFGQN AQFHYLYRS GFCIHVQCNA SKFHQGALLV AVLPEYVIGT VAGGTGTEDS HPPYKQTQPG ADGFELQHPY VLDAGIPISQ L TVCPHQWI NLRTNNCATI IVPYINALPF DSALNHCNFG LLVVPISPLD YDQGATPVIP ITITLAPMCS EFAGLRQ UniProtKB: Genome polyprotein |
-Macromolecule #3: VP3
Macromolecule | Name: VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Enterovirus A71 / Strain: Tainan/4643/98 |
Molecular weight | Theoretical: 25.811473 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
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 IPWISNTHYR AHARDGVFDY YTTGLVSIWY QTNYVVPIGA PNTAYIIALA AAQKNFTMQL CKDASDIL UniProtKB: Genome polyprotein |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
---|---|
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.2 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
---|---|
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: FIELD EMISSION GUN |
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 |