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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9642 | |||||||||
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Title | Cryo-EM structure of CVA10 mature virus | |||||||||
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![]() | picornavirus uncoating / receptor binding / VIRUS | |||||||||
Function / homology | ![]() symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 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 ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 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 / host cell cytoplasm / 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 / 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 | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
![]() | Zhu L / Sun Y | |||||||||
![]() | ![]() Title: Structures of Coxsackievirus A10 unveil the molecular mechanisms of receptor binding and viral uncoating. Authors: Ling Zhu / Yao Sun / Jinyan Fan / Bin Zhu / Lei Cao / Qiang Gao / Yanjun Zhang / Hongrong Liu / Zihe Rao / Xiangxi Wang / ![]() Abstract: Coxsackievirus A10 (CVA10), a human type-A Enterovirus (HEV-A), can cause diseases ranging from hand-foot-and-mouth disease to polio-myelitis-like disease. CVA10, together with some other HEV-As, ...Coxsackievirus A10 (CVA10), a human type-A Enterovirus (HEV-A), can cause diseases ranging from hand-foot-and-mouth disease to polio-myelitis-like disease. CVA10, together with some other HEV-As, utilizing the molecule KREMEN1 as an entry receptor, constitutes a KREMEN1-dependent subgroup within HEV-As. Currently, there is no vaccine or antiviral therapy available for treating diseases caused by CVA10. The atomic-resolution structure of the CVA10 virion, which is within the KREMEN1-dependent subgroup, shows significant conformational differences in the putative receptor binding sites and serotype-specific epitopes, when compared to the SCARB2-dependent subgroup of HEV-A, such as EV71, highlighting specific differences between the sub-groups. We also report two expanded structures of CVA10, an empty particle and uncoating intermediate at atomic resolution, as well as a medium-resolution genome structure reconstructed using a symmetry-mismatch method. Structural comparisons coupled with previous results, reveal an ordered signal transmission process for enterovirus uncoating, converting exo-genetic receptor-attachment inputs into a generic RNA release mechanism. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 167 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.5 KB 12.5 KB | Display Display | ![]() |
Images | ![]() | 253.7 KB | ||
Filedesc metadata | ![]() | 5.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 754.7 KB | Display | ![]() |
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Full document | ![]() | 754.3 KB | Display | |
Data in XML | ![]() | 6.9 KB | Display | |
Data in CIF | ![]() | 7.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6aksMC ![]() 9643C ![]() 9644C ![]() 9652C ![]() 6aktC ![]() 6akuC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Coxsackievirus A10
Entire | Name: ![]() ![]() |
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Components |
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-Supramolecule #1: Coxsackievirus A10
Supramolecule | Name: Coxsackievirus A10 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #2-#4 / NCBI-ID: 42769 / Sci species name: Coxsackievirus A10 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No |
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-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: ![]() ![]() |
Molecular weight | Theoretical: 33.101188 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: GDPVEDIIHD ALGSTARRAI SSATNVESAA NTTPSSHRLE TGRVPALQAA ETGATSNATD ENMIETRCVV NRNGVLETTI NHFFSRSGL VGVVNLTDGG TDTTGYVTWD IDIMGFVQLR RKCEMFTYMR FNAEFTFVTT TKNGEARPYM LQYMYVPPGA P KPTGRDAF ...String: GDPVEDIIHD ALGSTARRAI SSATNVESAA NTTPSSHRLE TGRVPALQAA ETGATSNATD ENMIETRCVV NRNGVLETTI NHFFSRSGL VGVVNLTDGG TDTTGYVTWD IDIMGFVQLR RKCEMFTYMR FNAEFTFVTT TKNGEARPYM LQYMYVPPGA P KPTGRDAF QWQTATNPSV FVKLTDPPAQ VSVPFMSPAS AYQWFYDGYP TFGQHPETSN TTYGLCPNNM MGTFAVRVVS RE ASQLKLQ TRVYMKLKHV RAWVPRPIRS QPYLLKNFPN YDSSKITNSA RDRSSIKQAN 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: ![]() ![]() |
Molecular weight | Theoretical: 27.783105 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: SPSVEACGYS DRVAQLTVGN SSITTQEAAN IVLAYGEWPE YCPDTDATAV DKPTRPDVSV NRFYTLDSKM WQENSTGWYW KFPDVLNKT GVFGQNAQFH YLYRSGFCLH VQCNASKFHQ GALLVAVIPE FVIAGRGSNT KPNEAPHPGF TTTFPGTTGA T FHDPYVLD ...String: SPSVEACGYS DRVAQLTVGN SSITTQEAAN IVLAYGEWPE YCPDTDATAV DKPTRPDVSV NRFYTLDSKM WQENSTGWYW KFPDVLNKT GVFGQNAQFH YLYRSGFCLH VQCNASKFHQ GALLVAVIPE FVIAGRGSNT KPNEAPHPGF TTTFPGTTGA T FHDPYVLD SGVPLSQALI YPHQWINLRT NNCATVIVPY INAVPFDSAI NHSNFGLIVI PVSPLKYSSG ATTAIPITIT IA PLNSEFG GLRQAVSQ 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: ![]() ![]() |
Molecular weight | Theoretical: 26.279826 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: GIPAELRPGT NQFLTTDDDT AAPILPGFTP TPTIHIPGEV HSLLELCRVE TILEVNNTTE ATGLTRLLIP VSSQNKADEL CAAFMVDPG RIGPWQSTLV GQICRYYTQW SGSLKVTFMF TGSFMATGKM LVAYSPPGSA QPANRETAML GTHVIWDFGL Q SSVSLVIP ...String: GIPAELRPGT NQFLTTDDDT AAPILPGFTP TPTIHIPGEV HSLLELCRVE TILEVNNTTE ATGLTRLLIP VSSQNKADEL CAAFMVDPG RIGPWQSTLV GQICRYYTQW SGSLKVTFMF TGSFMATGKM LVAYSPPGSA QPANRETAML GTHVIWDFGL Q SSVSLVIP WISNTHFRTA KTGGNYDYYT AGVVTLWYQT NYVVPPETPG EAYIIAMGAD LYKFTLKICK DTDEVTQQAV LQ 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: ![]() ![]() |
Molecular weight | Theoretical: 7.464104 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MGAQVSTQKS GSHETGNVAT GGSTINFTNI NYYKDSYAAS ATRQDFTQDP KKFTQPVLDS IRELSAPLN 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: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: EMDB MAP |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4586 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: ANGULAR RECONSTITUTION |