+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10256 | ||||||||||||
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Title | Structure of Coxsackievirus A10 A-particle | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | CV-A10 / KREMEN1 / Virus-receptor complex / Hand / foot and mouth disease / VIRUS / picornavirus uncoating intermediate | ||||||||||||
Function / homology | Function and homology information symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / protein complex oligomerization / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / monoatomic ion channel activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / protein complex oligomerization / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / monoatomic ion channel activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / 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 / 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 A10 | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 Å | ||||||||||||
Authors | Zhao Y / Zhou D | ||||||||||||
Funding support | United Kingdom, 3 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Hand-foot-and-mouth disease virus receptor KREMEN1 binds the canyon of Coxsackie Virus A10. Authors: Yuguang Zhao / Daming Zhou / Tao Ni / Dimple Karia / Abhay Kotecha / Xiangxi Wang / Zihe Rao / E Yvonne Jones / Elizabeth E Fry / Jingshan Ren / David I Stuart / Abstract: Coxsackievirus A10 (CV-A10) is responsible for an escalating number of severe infections in children, but no prophylactics or therapeutics are currently available. KREMEN1 (KRM1) is the entry ...Coxsackievirus A10 (CV-A10) is responsible for an escalating number of severe infections in children, but no prophylactics or therapeutics are currently available. KREMEN1 (KRM1) is the entry receptor for the largest receptor-group of hand-foot-and-mouth disease causing viruses, which includes CV-A10. We report here structures of CV-A10 mature virus alone and in complex with KRM1 as well as of the CV-A10 A-particle. The receptor spans the viral canyon with a large footprint on the virus surface. The footprint has some overlap with that seen for the neonatal Fc receptor complexed with enterovirus E6 but is larger and distinct from that of another enterovirus receptor SCARB2. Reduced occupancy of a particle-stabilising pocket factor in the complexed virus and the presence of both unbound and expanded virus particles suggests receptor binding initiates a cascade of conformational changes that produces expanded particles primed for viral uncoating. | ||||||||||||
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_10256.map.gz | 47.4 MB | EMDB map data format | |
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Header (meta data) | emd-10256-v30.xml emd-10256.xml | 12.1 KB 12.1 KB | Display Display | EMDB header |
Images | emd_10256.png | 287.7 KB | ||
Filedesc metadata | emd-10256.cif.gz | 5.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10256 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10256 | HTTPS FTP |
-Validation report
Summary document | emd_10256_validation.pdf.gz | 662.4 KB | Display | EMDB validaton report |
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Full document | emd_10256_full_validation.pdf.gz | 662 KB | Display | |
Data in XML | emd_10256_validation.xml.gz | 7 KB | Display | |
Data in CIF | emd_10256_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10256 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10256 | HTTPS FTP |
-Related structure data
Related structure data | 6snbMC 6smgC 6snwC 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_10256.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
-Sample components
-Entire : Coxsackievirus A10
Entire | Name: Coxsackievirus A10 |
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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: all / NCBI-ID: 42769 / Sci species name: Coxsackievirus A10 / Sci species strain: Kowalik / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Capsid protein VP1
Macromolecule | Name: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A |
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Source (natural) | Organism: Coxsackievirus A10 |
Molecular weight | Theoretical: 33.191422 KDa |
Sequence | String: GDPVEDIIHD ALSSTVRRAI TSGQDVNTAA GTAPSSHRLE TGRVPALQAA ETGATSNATD ENMIETRCVM NRNGVLEATI SHFFSRSGL VGVVNLTDGG TDTTGYAVWD IDIMGFVQLR RKCEMFTYMR FNAEFTFVTT TENGEARPFM LQYMYVPPGA P KPTGRDAF ...String: GDPVEDIIHD ALSSTVRRAI TSGQDVNTAA GTAPSSHRLE TGRVPALQAA ETGATSNATD ENMIETRCVM NRNGVLEATI SHFFSRSGL VGVVNLTDGG TDTTGYAVWD IDIMGFVQLR RKCEMFTYMR FNAEFTFVTT TENGEARPFM LQYMYVPPGA P KPTGRDAF QWQTATNPSV FVKLTDPPAQ VSVPFMSPAS AYQWFYDGYP TFGQHPETSN TTYGQCPNNM MGTFAVRVVS RV ASQLKLQ TRVYMKLKHV RAWIPRPIRS QPYLLKNFPN YDSSKITYSA RDRASIKQAN M UniProtKB: Genome polyprotein |
-Macromolecule #2: Capsid protein VP2
Macromolecule | Name: Capsid protein VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A |
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Source (natural) | Organism: Coxsackievirus A10 |
Molecular weight | Theoretical: 27.72998 KDa |
Sequence | String: SPSVEACGYS DRVAQLTVGN SSITTQEAAN IVLAYGEWPE YCPDTDATAV DKPTRPDVSV NRFYTLDSKM WQENSTGWYW KFPDVLNKT GVFGQNAQFH YLYRSGFCLH VQCNASKFHQ GALLVAVIPE FVLAGRGSNT KPNEAPHPGF NTTFPGTAGA S FNDPYVLD ...String: SPSVEACGYS DRVAQLTVGN SSITTQEAAN IVLAYGEWPE YCPDTDATAV DKPTRPDVSV NRFYTLDSKM WQENSTGWYW KFPDVLNKT GVFGQNAQFH YLYRSGFCLH VQCNASKFHQ GALLVAVIPE FVLAGRGSNT KPNEAPHPGF NTTFPGTAGA S FNDPYVLD SGVPLSQSLI YPHQWINLRT NNCATIIVPY INAVPFDSAI NHSNFGLIVV PVSPLKYSSG ATTAIPITVT IA PLNSEFG GLRQAVSQ UniProtKB: Genome polyprotein |
-Macromolecule #3: Capsid protein VP3
Macromolecule | Name: Capsid protein VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A |
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Source (natural) | Organism: Coxsackievirus A10 |
Molecular weight | Theoretical: 26.219672 KDa |
Sequence | String: GLPTELRPGT NQFLTTEDDT AAPILPGFSP TPSIHIPGEV RSLLELCRVE TILEVNNTTD ATGLNRLLIP VSAQNKADEL CAAFMVDPG RIGPWQSTLV GQICRYYTQW SGSLKVTFMF TGSFMATGKM LIAYSPPGSA QPANRETAML GTHVIWDFGL Q SSVSLVIP ...String: GLPTELRPGT NQFLTTEDDT AAPILPGFSP TPSIHIPGEV RSLLELCRVE TILEVNNTTD ATGLNRLLIP VSAQNKADEL CAAFMVDPG RIGPWQSTLV GQICRYYTQW SGSLKVTFMF TGSFMATGKM LIAYSPPGSA QPANRETAML GTHVIWDFGL Q SSVSLVIP WISNTHFRTA KTGGNYDYYT AGVVTLWYQT NYVVPPETPG EAYIIAMGAA QDNFTLKICK DTDEVTQQAV LQ UniProtKB: Genome polyprotein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Average electron dose: 35.0 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: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1578 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |