+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11166 | |||||||||
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Title | Coxsackievirus B3 in complex with capsid binder compound 17 | |||||||||
Map data | Coxsackie B3 virion in complex with compound 17 | |||||||||
Sample |
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Function / homology | Function and homology information : / symbiont-mediated perturbation of host gene expression / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 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-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid ...: / symbiont-mediated perturbation of host gene expression / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 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-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS 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 / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Coxsackievirus B3 (strain Nancy) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Domanska A / Flatt JW / Butcher SJ | |||||||||
Funding support | Finland, 2 items
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Citation | Journal: Commun Biol / Year: 2021 Title: Identification of a conserved virion-stabilizing network inside the interprotomer pocket of enteroviruses. Authors: Justin W Flatt / Aušra Domanska / Alma L Seppälä / Sarah J Butcher / Abstract: Enteroviruses pose a persistent and widespread threat to human physical health, with no specific treatments available. Small molecule capsid binders have the potential to be developed as antivirals ...Enteroviruses pose a persistent and widespread threat to human physical health, with no specific treatments available. Small molecule capsid binders have the potential to be developed as antivirals that prevent virus attachment and entry into host cells. To aid with broad-range drug development, we report here structures of coxsackieviruses B3 and B4 bound to different interprotomer-targeting capsid binders using single-particle cryo-EM. The EM density maps are beyond 3 Å resolution, providing detailed information about interactions in the ligand-binding pocket. Comparative analysis revealed the residues that form a conserved virion-stabilizing network at the interprotomer site, and showed the small molecule properties that allow anchoring in the pocket to inhibit virus disassembly. | |||||||||
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_11166.map.gz | 53.6 MB | EMDB map data format | |
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Header (meta data) | emd-11166-v30.xml emd-11166.xml | 13.8 KB 13.8 KB | Display Display | EMDB header |
Images | emd_11166.png | 287.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11166 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11166 | HTTPS FTP |
-Related structure data
Related structure data | 6zclMC 6zckC 6zmsC 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_11166.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Coxsackie B3 virion in complex with compound 17 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 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 : Coxsackievirus B3 (strain Nancy)
Entire | Name: Coxsackievirus B3 (strain Nancy) |
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Components |
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-Supramolecule #1: Coxsackievirus B3 (strain Nancy)
Supramolecule | Name: Coxsackievirus B3 (strain Nancy) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 Details: Virus was grown in Vero A cells and purified in CsCl gradient NCBI-ID: 103903 / Sci species name: Coxsackievirus B3 (strain Nancy) / Sci species strain: Nancy / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: human (human) |
Virus shell | Shell ID: 1 / Name: icasaheadron / Diameter: 300.0 Å / T number (triangulation number): 3 |
-Macromolecule #1: capsid protein VP1
Macromolecule | Name: capsid protein VP1 / type: protein_or_peptide / ID: 1 / Details: capsid protein VP1 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A |
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Source (natural) | Organism: Coxsackievirus B3 (strain Nancy) |
Molecular weight | Theoretical: 30.26893 KDa |
Sequence | String: RVADTVGTGP TNSEAIPALT AAETGHTSQV VPGDTMQTRH VKNYHSRSES TIENFLCRSA CVYFTEYKNS GAKRYAEWVL TPRQAAQLR RKLEFFTYVR FDLELTFVIT STQQPSTTQN QDAQILTHQI MYVPPGGPVP DKVDSYVWQT STNPSVFWTE G NAPPRMSI ...String: RVADTVGTGP TNSEAIPALT AAETGHTSQV VPGDTMQTRH VKNYHSRSES TIENFLCRSA CVYFTEYKNS GAKRYAEWVL TPRQAAQLR RKLEFFTYVR FDLELTFVIT STQQPSTTQN QDAQILTHQI MYVPPGGPVP DKVDSYVWQT STNPSVFWTE G NAPPRMSI PFLSIGNAYS NFYDGWSEFS RNGVYGINTL NNMGTLYARH VNAGSTGPIK STIRIYFKPK HVKAWIPRPP RL CQYEKAK NVNFQPSGVT TTRQSITTMT NT |
-Macromolecule #2: capsid protein VP2
Macromolecule | Name: capsid protein VP2 / type: protein_or_peptide / ID: 2 / Details: capsid protein VP2 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A |
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Source (natural) | Organism: Coxsackievirus B3 (strain Nancy) |
Molecular weight | Theoretical: 27.604205 KDa |
Sequence | String: SDRARSITLG NSTITTQECA NVVVGYGVWP DYLKDSEATA EDQPTQPDVA TCRFYTLDSV QWQKTSPGWW WKLPDALSNL GLFGQNMQY HYLGRTGYTV HVQCNASKFH QGCLLVVCVP EAEMGCATLD NTPSSAELLG GDTAKEFADK PVASGSNKLV Q RVVYNAGM ...String: SDRARSITLG NSTITTQECA NVVVGYGVWP DYLKDSEATA EDQPTQPDVA TCRFYTLDSV QWQKTSPGWW WKLPDALSNL GLFGQNMQY HYLGRTGYTV HVQCNASKFH QGCLLVVCVP EAEMGCATLD NTPSSAELLG GDTAKEFADK PVASGSNKLV Q RVVYNAGM GVGVGNLTIF PHQWINLRTN NSATIVMPYT NSVPMDNMFR HNNVTLMVIP FVPLDYCPGS TTYVPITVTI AP MCAEYNG LRLAG |
-Macromolecule #3: capsid protein VP3
Macromolecule | Name: capsid protein VP3 / type: protein_or_peptide / ID: 3 / Details: capsid protein VP3 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A |
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Source (natural) | Organism: Coxsackievirus B3 (strain Nancy) |
Molecular weight | Theoretical: 26.067596 KDa |
Sequence | String: GLPTMNTPGS CQFLTSDDFQ SPSAMPQYDV TPEMRIPGEV KNLMEIAEVD SVVPVQNVGE KVNSMEAYQI PVRSNEGSGT QVFGFPLQP GYSSVFSRTL LGEILNYYTH WSGSIKLTFM FCGSAMATGK FLLAYSPPGA GAPTKRVDAM LGTHVIWDVG L QSSCVLCI ...String: GLPTMNTPGS CQFLTSDDFQ SPSAMPQYDV TPEMRIPGEV KNLMEIAEVD SVVPVQNVGE KVNSMEAYQI PVRSNEGSGT QVFGFPLQP GYSSVFSRTL LGEILNYYTH WSGSIKLTFM FCGSAMATGK FLLAYSPPGA GAPTKRVDAM LGTHVIWDVG L QSSCVLCI PWISQTHYRF VASDEYTAGG FITCWYQTNI VVPADAQSSC YIMCFVSACN DFSVRLLKDT PFISQQNFF |
-Macromolecule #4: capsid protein VP4
Macromolecule | Name: capsid protein VP4 / type: protein_or_peptide / ID: 4 / Details: myristoylated peptide, capsid protein VP4 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A |
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Source (natural) | Organism: Coxsackievirus B3 (strain Nancy) |
Molecular weight | Theoretical: 7.449181 KDa |
Sequence | String: GAQVSTQKTG AHETRLNASG NSIIHYTNIN YYKDAASNSA NRQDFTQDPG KFTEPVKDIM IKSLPALN |
-Macromolecule #5: 4-[[4-[1,3-bis(oxidanylidene)isoindol-2-yl]phenyl]sulfonylamino]b...
Macromolecule | Name: 4-[[4-[1,3-bis(oxidanylidene)isoindol-2-yl]phenyl]sulfonylamino]benzoic acid type: ligand / ID: 5 / Number of copies: 1 / Formula: FHK |
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Molecular weight | Theoretical: 422.411 Da |
Chemical component information | ChemComp-FHK: |
-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: 7.5 |
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Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
Details | Purified virus was mixed with compound 17 and incubated at room temperature for 30 min before plunging |
-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: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 47.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 18626 |