+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0855 | |||||||||
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Title | Cryo-EM structure of full echovirus 11 particle at pH 5.5 | |||||||||
Map data | Cryo-EM structure of full echovirus 11 particle at pH 5.5 | |||||||||
Sample |
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Keywords | Cryo-EM structure / echovirus 11 / full particle / pH 5.5 / 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 / 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 RIG-I 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 gene expression / nucleoside-triphosphate phosphatase / viral capsid / monoatomic ion transmembrane transport / host cell cytoplasm / DNA replication / RNA helicase activity / induction by virus of host autophagy / symbiont entry into host cell / 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 / cytoplasm Similarity search - Function | |||||||||
Biological species | Echovirus E11 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.34 Å | |||||||||
Authors | Liu S / Gao FG | |||||||||
Citation | Journal: Chin.Sci.Bull. / Year: 2020 Title: Molecular and structural basis of Echovirus 11 infection by using the dual-receptor system of CD55 and FcRn. Authors: Niu S / Liu C / Liu C / Liu S / Song Y / Zhang Y / Tian W / Zhao X / Wang P / Gao FG | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0855.map.gz | 196.5 MB | EMDB map data format | |
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Header (meta data) | emd-0855-v30.xml emd-0855.xml | 11.5 KB 11.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0855_fsc.xml | 13.5 KB | Display | FSC data file |
Images | emd_0855.png | 275.8 KB | ||
Filedesc metadata | emd-0855.cif.gz | 5.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0855 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0855 | HTTPS FTP |
-Validation report
Summary document | emd_0855_validation.pdf.gz | 769.9 KB | Display | EMDB validaton report |
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Full document | emd_0855_full_validation.pdf.gz | 769.5 KB | Display | |
Data in XML | emd_0855_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | emd_0855_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0855 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0855 | HTTPS FTP |
-Related structure data
Related structure data | 6la4MC 0854C 0856C 0857C 0858C 0859C 0860C 0867C 0870C 0871C 6la3C 6la5C 6la6C 6la7C 6laoC 6lapC 6lb1C 6lboC 6lbqC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0855.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of full echovirus 11 particle at pH 5.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Echovirus E11
Entire | Name: Echovirus E11 |
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Components |
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-Supramolecule #1: Echovirus E11
Supramolecule | Name: Echovirus E11 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #2-#4 / NCBI-ID: 12078 / Sci species name: Echovirus E11 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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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: Echovirus E11 |
Molecular weight | Theoretical: 32.277359 KDa |
Sequence | String: VVEAVENAVA RVADTISSGP SNSQAVPALT AVETGHTSQV TPSDTIQTRH VRNYHSRSES SIENFLCRSA CVYMGEYHTT NTDTSKLFA SWTINARRMV QMRRKLELFT YVRFDMEVTF VITSKQDQGT QLGQDMPPLT HQIMYIPPGG PIPKSVTDYT W QTSTNPSI ...String: VVEAVENAVA RVADTISSGP SNSQAVPALT AVETGHTSQV TPSDTIQTRH VRNYHSRSES SIENFLCRSA CVYMGEYHTT NTDTSKLFA SWTINARRMV QMRRKLELFT YVRFDMEVTF VITSKQDQGT QLGQDMPPLT HQIMYIPPGG PIPKSVTDYT W QTSTNPSI FWTEGNAPPR MSIPFISIGN AYSNFYDGWS HFSQNGVYGY NTLNHMGQIY VRHVNGSSPL PMTSTVRMYF KP KHVKVWV PRPPRLCQYK NASTVNFTPT NITEKRQSIN YIPETVKP |
-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: Echovirus E11 |
Molecular weight | Theoretical: 27.968449 KDa |
Sequence | String: DRVRSITLGN STITTQESAN VVVAYGRWPE YLKDNEATAE DQPTQPDVAT CRFYTLESVT WERDSPGWWW KFPDALKDMG LFGQNMYYH YLGRAGYTIH VQCNASKFHQ GCLMVVCVPE AEMGCSQVDG TVNEHSLSEG ETAKKFASTS TNGTNTVQSI V TNAGMGVG ...String: DRVRSITLGN STITTQESAN VVVAYGRWPE YLKDNEATAE DQPTQPDVAT CRFYTLESVT WERDSPGWWW KFPDALKDMG LFGQNMYYH YLGRAGYTIH VQCNASKFHQ GCLMVVCVPE AEMGCSQVDG TVNEHSLSEG ETAKKFASTS TNGTNTVQSI V TNAGMGVG VGNLTIFPHQ WINLRTNNCA TIVMPYINNV PMDNMFRHHN FTLMIIPFVP LDYSSDSSTY VPITVTVAPM CA EYNGLRL ATSL |
-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: Echovirus E11 |
Molecular weight | Theoretical: 26.062578 KDa |
Sequence | String: GLPVMNTPGS NQFLTSDDFQ SPSAMPQFDV TPELNIPGEV QNLMEIAEVD SVVPVNNVEG KLDTMEIYRI PVQSGNHQSS QVFGFQVQP GLDNVFKHTL LGEILNYYAH WSGSIKLTFV FCGSAMATGK FLLAYAPPGA NAPKSRKDAM LGTHIIWDVG L QSSCVLCI ...String: GLPVMNTPGS NQFLTSDDFQ SPSAMPQFDV TPELNIPGEV QNLMEIAEVD SVVPVNNVEG KLDTMEIYRI PVQSGNHQSS QVFGFQVQP GLDNVFKHTL LGEILNYYAH WSGSIKLTFV FCGSAMATGK FLLAYAPPGA NAPKSRKDAM LGTHIIWDVG L QSSCVLCI PWISQTHYRL VQQDEYTSAG NVTCWYQTGI VVPAGTPTSC SIMCFVSACN DFSVRLLKDT PFIEQSALLQ |
-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: Echovirus E11 |
Molecular weight | Theoretical: 7.495273 KDa |
Sequence | String: MGAQVSTQKT GAHETGLNAS GRSIIHYTNI NYYKDAASNS ANRQDFSQDP GKFTEPVKDI MVKSLPALN |
-Macromolecule #5: SPHINGOSINE
Macromolecule | Name: SPHINGOSINE / type: ligand / ID: 5 / Number of copies: 1 / Formula: SPH |
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Molecular weight | Theoretical: 299.492 Da |
Chemical component information | ChemComp-SPH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 5.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 1.025 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |