+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32575 | |||||||||
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Title | CVB5 expended empty particle | |||||||||
Map data | ||||||||||
Sample |
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Keywords | CVB5 E-particle / 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 / 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 / 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 / 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 / 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 Similarity search - Function | |||||||||
Biological species | Coxsackievirus B5 | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 2.95 Å | |||||||||
Authors | Yang P / Wang K | |||||||||
Funding support | China, 1 items
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Citation | Journal: J Virol / Year: 2022 Title: Atomic Structures of Coxsackievirus B5 Provide Key Information on Viral Evolution and Survival. Authors: Peng Yang / Dawei Shi / Jianmeng Fu / Li Zhang / Ruihong Chen / Binyang Zheng / Xiangxi Wang / Sihong Xu / Ling Zhu / Kang Wang / Abstract: Coxsackie virus B5 (CVB5), a main serotype in human Enterovirus B (EVB), can cause severe viral encephalitis and aseptic meningitis among infants and children. Currently, there is no approved vaccine ...Coxsackie virus B5 (CVB5), a main serotype in human Enterovirus B (EVB), can cause severe viral encephalitis and aseptic meningitis among infants and children. Currently, there is no approved vaccine or antiviral therapy available against CVB5 infection. Here, we determined the atomic structures of CVB5 in three forms: mature full (F) particle (2.73 Å), intermediate altered (A) particle (2.81 Å), and procapsid empty (E) particle (2.95 Å). Structural analysis of F particle of CVB5 unveiled similar structures of "canyon," "puff," and "knob" as those other EV-Bs. We observed structural rearrangements that are alike during the transition from F to A particle, indicative of similar antigenicity, cell entry, and uncoating mechanisms shared by all EV-Bs. Further comparison of structures and sequences among all structure-known EV-Bs revealed that while the residues targeted by neutralizing MAbs are diversified and drive the evolution of EV-Bs, the relative conserved residues recognized by uncoating receptors could serve as the basis for the development of antiviral vaccines and therapeutics. As one of the main serotypes in Enterovirus B, CVB5 has been commonly reported in recent years. The atomic structures of CVB5 shown here revealed classical features found in EV-Bs and the structural rearrangement occurring during particle expansion and uncoating. Also, structure- and sequence-based comparison between CVB5 and other structure-known EV-Bs screened out key domains important for viral evolution and survival. All these provide insights into the development of vaccine and therapeutics for EV-Bs. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32575.map.gz | 166.9 MB | EMDB map data format | |
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Header (meta data) | emd-32575-v30.xml emd-32575.xml | 12 KB 12 KB | Display Display | EMDB header |
Images | emd_32575.png | 51.4 KB | ||
Filedesc metadata | emd-32575.cif.gz | 5.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32575 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32575 | HTTPS FTP |
-Validation report
Summary document | emd_32575_validation.pdf.gz | 751.6 KB | Display | EMDB validaton report |
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Full document | emd_32575_full_validation.pdf.gz | 751.2 KB | Display | |
Data in XML | emd_32575_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | emd_32575_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32575 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32575 | HTTPS FTP |
-Related structure data
Related structure data | 7wl3MC 7xb2C 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_32575.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.329 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Coxsackievirus B5
Entire | Name: Coxsackievirus B5 |
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Components |
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-Supramolecule #1: Coxsackievirus B5
Supramolecule | Name: Coxsackievirus B5 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12074 / Sci species name: Coxsackievirus B5 / Virus type: VIROID / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes |
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Virus shell | Shell ID: 1 / Diameter: 339.9 Å |
-Macromolecule #1: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Coxsackievirus B5 |
Molecular weight | Theoretical: 25.928107 KDa |
Sequence | String: NYHSRSESTV ENFLCRSACV FYTTYRNHGT DGDNFGYWVI NTRQVAQLRR KLEMFTYARF DLELTFVITS TQEQSTIQGQ DSPVLTHQI MYVPPGGPVP TKVNSYSWQT STNPSVFWTE GSAPPRMSIP FISIGNAYSM FYDGWAKFDK QGTYGINTLN N MGTLYMRH ...String: NYHSRSESTV ENFLCRSACV FYTTYRNHGT DGDNFGYWVI NTRQVAQLRR KLEMFTYARF DLELTFVITS TQEQSTIQGQ DSPVLTHQI MYVPPGGPVP TKVNSYSWQT STNPSVFWTE GSAPPRMSIP FISIGNAYSM FYDGWAKFDK QGTYGINTLN N MGTLYMRH VNDGSPGPIV STVRIYFKPK HVKTWVPRPP RLCQYQKAGN VNFEPTGVTE SRTDITTMQ UniProtKB: Genome polyprotein |
-Macromolecule #2: Genome polyprotein
Macromolecule | Name: Genome polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A |
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Source (natural) | Organism: Coxsackievirus B5 |
Molecular weight | Theoretical: 27.185674 KDa |
Sequence | String: RVRSITLGNS TITTQECANV VVGYGVWPTY LNDDEATAED QPTQPDVATC RFYTLESVMW QQSSPGWWWK FPDALSNMGL FGQNMQYHY LGRAGYTVHV QCNASKFHQG CLLVVCVPEA EMGCATLANK PDQKSLSNGE TANMFESQNS TGQTAVQANV I NAGMGVGV ...String: RVRSITLGNS TITTQECANV VVGYGVWPTY LNDDEATAED QPTQPDVATC RFYTLESVMW QQSSPGWWWK FPDALSNMGL FGQNMQYHY LGRAGYTVHV QCNASKFHQG CLLVVCVPEA EMGCATLANK PDQKSLSNGE TANMFESQNS TGQTAVQANV I NAGMGVGV GNLTIFPHQW INLRTNNSAT IVMPYINSVP MDNMFRHNNF TLMIIPFAPL SYSTGATTYV PITVTVAPMC AE YNGLRLA UniProtKB: Genome polyprotein |
-Macromolecule #3: Genome polyprotein
Macromolecule | Name: Genome polyprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A |
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Source (natural) | Organism: Coxsackievirus B5 |
Molecular weight | Theoretical: 26.163672 KDa |
Sequence | String: GLPTMLTPGS NQFLTSDDFQ SPSAMPQFDV TPEMDIPGQV NNLMEIAEVD SVVPVNNTEG KVLSIESYQI PVQSNSTNGS QVFGFPLMP GASSVLNRTL LGEILNYYTH WSGSIKLTFM FCGSAMATGK FLLAYSPPGA GAPTTRKEAM LGTHVIWDVG L QSSCVLCI ...String: GLPTMLTPGS NQFLTSDDFQ SPSAMPQFDV TPEMDIPGQV NNLMEIAEVD SVVPVNNTEG KVLSIESYQI PVQSNSTNGS QVFGFPLMP GASSVLNRTL LGEILNYYTH WSGSIKLTFM FCGSAMATGK FLLAYSPPGA GAPTTRKEAM LGTHVIWDVG L QSSCVLCI PWISQTHYRY VVVDEYTAGG YITCWYQTNI VVPADTQSDC KILCFVSACN DFSVRMLKDT PFIKQDNFYQ UniProtKB: Genome polyprotein |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.4 |
Staining | Type: NEGATIVE / Material: Phosphotungstic acid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: DIFFRACTION / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14497 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-7wl3: |