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Yorodumi- EMDB-50930: Rhinovirus A2 uncoating intermediate revealing the natural pocket... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-50930 | |||||||||
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Title | Rhinovirus A2 uncoating intermediate revealing the natural pocket factor (pH 5.8 and 4 degrees Celsius) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Uncoating Intermediate / Pocket Factor / Lauric Acid / VIRUS | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Real-Hohn A / Blaas D | |||||||||
Funding support | Austria, 1 items
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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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_50930.map.gz | 88.4 MB | EMDB map data format | |
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Header (meta data) | emd-50930-v30.xml emd-50930.xml | 20 KB 20 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_50930_fsc.xml | 20.4 KB | Display | FSC data file |
Images | emd_50930.png | 127.7 KB | ||
Filedesc metadata | emd-50930.cif.gz | 6.4 KB | ||
Others | emd_50930_half_map_1.map.gz emd_50930_half_map_2.map.gz | 273.6 MB 273.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-50930 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-50930 | HTTPS FTP |
-Validation report
Summary document | emd_50930_validation.pdf.gz | 1000.3 KB | Display | EMDB validaton report |
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Full document | emd_50930_full_validation.pdf.gz | 999.8 KB | Display | |
Data in XML | emd_50930_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | emd_50930_validation.cif.gz | 30.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50930 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50930 | HTTPS FTP |
-Related structure data
Related structure data | 9g0bMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_50930.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.998 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_50930_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_50930_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : rhinovirus A2
Entire | Name: rhinovirus A2 |
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Components |
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-Supramolecule #1: rhinovirus A2
Supramolecule | Name: rhinovirus A2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / NCBI-ID: 12130 / Sci species name: rhinovirus A2 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Homo sapiens (human) |
Virus shell | Shell ID: 1 / Diameter: 310.0 Å / T number (triangulation number): 3 |
-Macromolecule #1: Capsid protein VP1
Macromolecule | Name: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: rhinovirus A2 |
Molecular weight | Theoretical: 32.2741 KDa |
Sequence | String: NPVENYIDEV LNEVLVVPNI NSSNPTTSNS APALDAAETG HTSSVQPEDV IETRYVQTSQ TRDEMSLESF LGRSGCIHES KLEVTLANY NKENFTVWAI NLQEMAQIRR KFELFTYTRF DSEITLVPCI SALSQDIGHI TMQYMYVPPG APVPNSRDDY A WQSGTNAS ...String: NPVENYIDEV LNEVLVVPNI NSSNPTTSNS APALDAAETG HTSSVQPEDV IETRYVQTSQ TRDEMSLESF LGRSGCIHES KLEVTLANY NKENFTVWAI NLQEMAQIRR KFELFTYTRF DSEITLVPCI SALSQDIGHI TMQYMYVPPG APVPNSRDDY A WQSGTNAS VFWQHGQAYP RFSLPFLSVA SAYYMFYDGY DEQDQNYGTA NTNNMGSLCS RIVTEKHIHK VHIMTRIYHK AK HVKAWCP RPPRALEYTR AHRTNFKIED RSIQTAIVTR PIITTA UniProtKB: Genome polyprotein |
-Macromolecule #2: Capsid protein VP2
Macromolecule | Name: Capsid protein VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: rhinovirus A2 |
Molecular weight | Theoretical: 29.009588 KDa |
Sequence | String: SPTVEACGYS DRIIQITRGD STITSQDVAN AIVAYGVWPH YLSSKDASAI DKPSQPDTSS NRFYTLRSVT WSSSSKGWWW KLPDALKDM GIFGENMFYH YLGRSGYTIH VQCNASKFHQ GTLIVALIPE HQIASALHGN VNVGYNYTHP GETGREVKAE T RLNPDLQP ...String: SPTVEACGYS DRIIQITRGD STITSQDVAN AIVAYGVWPH YLSSKDASAI DKPSQPDTSS NRFYTLRSVT WSSSSKGWWW KLPDALKDM GIFGENMFYH YLGRSGYTIH VQCNASKFHQ GTLIVALIPE HQIASALHGN VNVGYNYTHP GETGREVKAE T RLNPDLQP TEEYWLNFDG TLLGNITIFP HQFINLRSNN SATIIAPYVN AVPMDSMRSH NNWSLVIIPI CPLETSSAIN TI PITISIS PMCAEFSGAR AKRQ UniProtKB: Genome polyprotein |
-Macromolecule #3: Capsid protein VP3
Macromolecule | Name: Capsid protein VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: rhinovirus A2 |
Molecular weight | Theoretical: 26.107793 KDa |
Sequence | String: GLPVFITPGS GQFLTTDDFQ SPCALPWYHP TKEISIPGEV KNLVEICQVD SLVPINNTDT YINSENMYSV VLQSSINAPD KIFSIRTDV ASQPLATTLI GEISSYFTHW TGSLRFSFMF CGTANTTVKL LLAYTPPGIA EPTTRKDAML GTHVIWDVGL Q STISMVVP ...String: GLPVFITPGS GQFLTTDDFQ SPCALPWYHP TKEISIPGEV KNLVEICQVD SLVPINNTDT YINSENMYSV VLQSSINAPD KIFSIRTDV ASQPLATTLI GEISSYFTHW TGSLRFSFMF CGTANTTVKL LLAYTPPGIA EPTTRKDAML GTHVIWDVGL Q STISMVVP WISASHYRNT SPGRSTSGYI TCWYQTRLVI PPQTPPTARL LCFVSGCKDF CLRMARDTNL HLQSGAIAQ UniProtKB: Genome polyprotein |
-Macromolecule #4: Capsid protein VP4
Macromolecule | Name: Capsid protein VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: rhinovirus A2 |
Molecular weight | Theoretical: 7.356971 KDa |
Sequence | String: GAQVSRQNVG THSTQNSVSN GSSLNYFNIN YFKDAASNGA SKLEFTQDPS KFTDPVKDVL EKGIPTLQ UniProtKB: Genome polyprotein |
-Macromolecule #5: LAURIC ACID
Macromolecule | Name: LAURIC ACID / type: ligand / ID: 5 / Number of copies: 1 / Formula: DAO |
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Molecular weight | Theoretical: 200.318 Da |
Chemical component information | ChemComp-DAO: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL | |||||||||
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Buffer | pH: 5.8 Component:
Details: 0.1 M phosphate buffer, pH 5.8 | |||||||||
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 293 K / Instrument: LEICA EM GP | |||||||||
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. |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 2 / Number real images: 246 / Average electron dose: 60.0 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: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 100000 |
Sample stage | Cooling holder cryogen: NITROGEN |