+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30320 | |||||||||
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Title | Echovirus 3 F-particle | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Echovirus B / mature / 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 ...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 / viral capsid / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host gene expression / DNA replication / RNA helicase activity / symbiont entry into host cell / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Echovirus E3 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Wang K / Rao Z | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Structures of Echovirus 30 in complex with its receptors inform a rational prediction for enterovirus receptor usage. Authors: Kang Wang / Ling Zhu / Yao Sun / Minhao Li / Xin Zhao / Lunbiao Cui / Li Zhang / George F Gao / Weiwei Zhai / Fengcai Zhu / Zihe Rao / Xiangxi Wang / Abstract: Receptor usage that determines cell tropism and drives viral classification closely correlates with the virus structure. Enterovirus B (EV-B) consists of several subgroups according to receptor ...Receptor usage that determines cell tropism and drives viral classification closely correlates with the virus structure. Enterovirus B (EV-B) consists of several subgroups according to receptor usage, among which echovirus 30 (E30), a leading causative agent for human aseptic meningitis, utilizes FcRn as an uncoating receptor. However, receptors for many EVs remain unknown. Here we analyzed the atomic structures of E30 mature virion, empty- and A-particles, which reveals serotype-specific epitopes and striking conformational differences between the subgroups within EV-Bs. Of these, the VP1 BC loop markedly distinguishes E30 from other EV-Bs, indicative of a role as a structural marker for EV-B. By obtaining cryo-electron microscopy structures of E30 in complex with its receptor FcRn and CD55 and comparing its homologs, we deciphered the underlying molecular basis for receptor recognition. Together with experimentally derived viral receptor identifications, we developed a structure-based in silico algorithm to inform a rational prediction for EV receptor usage. | |||||||||
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_30320.map.gz | 115.3 MB | EMDB map data format | |
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Header (meta data) | emd-30320-v30.xml emd-30320.xml | 15.1 KB 15.1 KB | Display Display | EMDB header |
Images | emd_30320.png | 116.9 KB | ||
Filedesc metadata | emd-30320.cif.gz | 6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30320 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30320 | HTTPS FTP |
-Related structure data
Related structure data | 7c9xMC 7c9sC 7c9tC 7c9uC 7c9vC 7c9wC 7c9yC 7c9zC 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_30320.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.347 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 E3
Entire | Name: Echovirus E3 |
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Components |
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-Supramolecule #1: Echovirus E3
Supramolecule | Name: Echovirus E3 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 Details: Particles purified from the cell cultures innoculated with the live E3. NCBI-ID: 47516 / Sci species name: Echovirus E3 / 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: 30.0 Å / T number (triangulation number): 3 |
-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: Echovirus E3 |
Molecular weight | Theoretical: 31.761631 KDa |
Sequence | String: GDVEEAIDRA VARVADTMPT GPRNTESVPA LTAVETGHTS QVVPGDTMQT RHVKNYHSRT ESSIENFLCR AACVYIATYK SAGGTPTER YASWRINTRQ MVQLRRKFEL FTYLRFDMEI TFVITSTQDP GTQLAQDMPV LTHQIMYIPP GGPVPNSATD F AWQSSTNP ...String: GDVEEAIDRA VARVADTMPT GPRNTESVPA LTAVETGHTS QVVPGDTMQT RHVKNYHSRT ESSIENFLCR AACVYIATYK SAGGTPTER YASWRINTRQ MVQLRRKFEL FTYLRFDMEI TFVITSTQDP GTQLAQDMPV LTHQIMYIPP GGPVPNSATD F AWQSSTNP SIFWTEGCAP ARMSVPFISI GNAYSNFYDG WSHFTQEGVY GFNSLNNMGH IYVRHVNEQS LGVSTSTLRV YF KPKHVRA WVPRPPRLSP YVKSSNVNFK PTAVTTERKD INDVGT UniProtKB: Genome polyprotein |
-Macromolecule #2: VP2
Macromolecule | Name: VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Echovirus E3 |
Molecular weight | Theoretical: 29.221725 KDa |
Sequence | String: SPTVEECGFS DRVRSITLGN STITTQECAN VVVGYGVWPS YLQDNEATAE DQPTQPDVAT CRFYTLDSIQ WQKESDGWWW KFPEALKNM GLFGQNMEYH YLGRSGYTIH VQCNASKFHQ GCLLVVCVPE AEMGCSDVER EVVAASLSSE DTAKSFSRTE S NGQHTVQT ...String: SPTVEECGFS DRVRSITLGN STITTQECAN VVVGYGVWPS YLQDNEATAE DQPTQPDVAT CRFYTLDSIQ WQKESDGWWW KFPEALKNM GLFGQNMEYH YLGRSGYTIH VQCNASKFHQ GCLLVVCVPE AEMGCSDVER EVVAASLSSE DTAKSFSRTE S NGQHTVQT VVYNAGMGVG VGNLTIFPHQ WINLRTNNSA TIVMPYINSV PMDNMFRHYN FTLMIIPFAK LEYTEQASNY VP ITVTVAP MCAEYNGLRL ASHQ 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: Echovirus E3 |
Molecular weight | Theoretical: 26.281973 KDa |
Sequence | String: GLPTMLTPGS NQFLTSDDFQ SPSAMPQFDV TPEMKIPGEV HNLMEIAEVD SVVPVNNTKE NINSMEAYRI PVTGGDQLHT QVFGFQMQP GLNSVFKRTL LGEILNYYAH WSGSVKLTFV FCGSAMATGK FLLAYSPPGA SPPQNRKQAM LGTHVIWDVG L QSSCVLCI ...String: GLPTMLTPGS NQFLTSDDFQ SPSAMPQFDV TPEMKIPGEV HNLMEIAEVD SVVPVNNTKE NINSMEAYRI PVTGGDQLHT QVFGFQMQP GLNSVFKRTL LGEILNYYAH WSGSVKLTFV FCGSAMATGK FLLAYSPPGA SPPQNRKQAM LGTHVIWDVG L QSSCVLCI PWISQTHYRL VQQDEYTSAG YVTCWYQTGL IVPPGAPPSC TILCFASACN DFSVRMLRDT PFIEQTQLLQ UniProtKB: Genome polyprotein |
-Macromolecule #4: VP4
Macromolecule | Name: VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Echovirus E3 |
Molecular weight | Theoretical: 7.402076 KDa |
Sequence | String: GAQVSTQKTG AHETSLTASG NSTIHYTNIN YYKDAASNSA NRQDFTQDPS KFTEPMKDVM IKSLPALN UniProtKB: Genome polyprotein |
-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: |
-Macromolecule #6: MYRISTIC ACID
Macromolecule | Name: MYRISTIC ACID / type: ligand / ID: 6 / Number of copies: 1 / Formula: MYR |
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Molecular weight | Theoretical: 228.371 Da |
Chemical component information | ChemComp-MYR: |
-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 R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK I |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 30.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |
Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 5000 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-7c9x: |