+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15711 | |||||||||
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Title | Human rhinovirus 2 empty particle in situ | |||||||||
Map data | EM map after pixel size scaling presented in 2-fold on Z (MRC standard) orientation. Micrographs were collected on lamellipodia of Cos7 cells infected with HRV2. | |||||||||
Sample |
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Keywords | Human rhinovirus 2 / empty particle / in situ / cryo-EM. / 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 / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host gene expression / 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: 7.1 Å | |||||||||
Authors | Ishemgulova A / Mukhamedova L / Trebichalska Z / Payne P / Smerdova L / Moravcova J / Hrebik D / Buchta D / Skubnik K / Fuzik T ...Ishemgulova A / Mukhamedova L / Trebichalska Z / Payne P / Smerdova L / Moravcova J / Hrebik D / Buchta D / Skubnik K / Fuzik T / Novacek J / Plevka P | |||||||||
Funding support | Czech Republic, 1 items
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Citation | Journal: To Be Published Title: Endosome rupture enables enteroviruses to infect cells. Authors: Ishemgulova A | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15711.map.gz | 4.4 MB | EMDB map data format | |
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Header (meta data) | emd-15711-v30.xml emd-15711.xml | 17.4 KB 17.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15711_fsc.xml | 8 KB | Display | FSC data file |
Images | emd_15711.png | 120.8 KB | ||
Others | emd_15711_half_map_1.map.gz emd_15711_half_map_2.map.gz | 30.7 MB 30.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15711 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15711 | HTTPS FTP |
-Validation report
Summary document | emd_15711_validation.pdf.gz | 859.2 KB | Display | EMDB validaton report |
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Full document | emd_15711_full_validation.pdf.gz | 858.7 KB | Display | |
Data in XML | emd_15711_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | emd_15711_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15711 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15711 | HTTPS FTP |
-Related structure data
Related structure data | 8ay5MC 8ay4C 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_15711.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | EM map after pixel size scaling presented in 2-fold on Z (MRC standard) orientation. Micrographs were collected on lamellipodia of Cos7 cells infected with HRV2. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.64784 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: EM half map before pixel size scaling presented...
File | emd_15711_half_map_1.map | ||||||||||||
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Annotation | EM half map before pixel size scaling presented in 2-fold on Z (MRC standard) orientation. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: EM half map before pixel size scaling presented...
File | emd_15711_half_map_2.map | ||||||||||||
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Annotation | EM half map before pixel size scaling presented in 2-fold on Z (MRC standard) orientation. | ||||||||||||
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: all / NCBI-ID: 12130 / Sci species name: rhinovirus A2 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes |
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-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: 28.851441 KDa |
Sequence | String: ALDAAETGHT SSVQPEDVIE TRYVQTSQTR DEMSLESFLG RSGCIHESKL EVTLANYNKE NFTVWAINLQ EMAQIRRKFE LFTYTRFDS EITLVPCISA LSQDIGHITM QYMYVPPGAP VPNSRDDYAW QSGTNASVFW QHGQAYPRFS LPFLSVASAY Y MFYDGYDE ...String: ALDAAETGHT SSVQPEDVIE TRYVQTSQTR DEMSLESFLG RSGCIHESKL EVTLANYNKE NFTVWAINLQ EMAQIRRKFE LFTYTRFDS EITLVPCISA LSQDIGHITM QYMYVPPGAP VPNSRDDYAW QSGTNASVFW QHGQAYPRFS LPFLSVASAY Y MFYDGYDE QDQNYGTANT NNMGSLCSRI VTEKHIHKVH IMTRIYHKAK HVKAWCPRPP RALEYTRAHR TNFKIEDRSI QT AIVTRPI ITTA 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: 27.899426 KDa |
Sequence | String: RIIQITRGDS TITSQDVANA IVAYGVWPHY LSSKDASAID KPSQPDTSSN RFYTLRSVTW SSSSKGWWWK LPDALKDMGI FGENMFYHY LGRSGYTIHV QCNASKFHQG TLIVALIPEH QIASALHGNV NVGYNYTHPG ETGREVKAET RLNPDLQPTE E YWLNFDGT ...String: RIIQITRGDS TITSQDVANA IVAYGVWPHY LSSKDASAID KPSQPDTSSN RFYTLRSVTW SSSSKGWWWK LPDALKDMGI FGENMFYHY LGRSGYTIHV QCNASKFHQG TLIVALIPEH QIASALHGNV NVGYNYTHPG ETGREVKAET RLNPDLQPTE E YWLNFDGT LLGNITIFPH QFINLRSNNS ATIIAPYVNA VPMDSMRSHN NWSLVIIPIC PLETSSAINT IPITISISPM CA EFSGARA KRQ 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: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average exposure time: 10.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-8ay5: |