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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-30805 | |||||||||
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Title | Cryo-EM structure of Coxsackievirus B1 mature virion | |||||||||
![]() | Cryo-EM structure of Coxsackievirus B1 mature virion | |||||||||
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![]() | Coxsackievirus B1 / mature virion / Cryo-EM / VIRUS | |||||||||
Function / homology | ![]() 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 gene expression ...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 gene expression / viral capsid / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / DNA replication / host cell cytoplasm / RNA helicase activity / symbiont entry into host cell / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / 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: 3.2 Å | |||||||||
![]() | Zheng Q / Li S | |||||||||
![]() | ![]() Title: Cryo-EM structures reveal the molecular basis of receptor-initiated coxsackievirus uncoating. Authors: Longfa Xu / Qingbing Zheng / Rui Zhu / Zhichao Yin / Hai Yu / Yu Lin / Yuanyuan Wu / Maozhou He / Yang Huang / Yichao Jiang / Hui Sun / Zhenghui Zha / Hongwei Yang / Qiongzi Huang / Dongqing ...Authors: Longfa Xu / Qingbing Zheng / Rui Zhu / Zhichao Yin / Hai Yu / Yu Lin / Yuanyuan Wu / Maozhou He / Yang Huang / Yichao Jiang / Hui Sun / Zhenghui Zha / Hongwei Yang / Qiongzi Huang / Dongqing Zhang / Zhenqin Chen / Xiangzhong Ye / Jinle Han / Lisheng Yang / Che Liu / Yuqiong Que / Mujin Fang / Ying Gu / Jun Zhang / Wenxin Luo / Z Hong Zhou / Shaowei Li / Tong Cheng / Ningshao Xia / ![]() ![]() Abstract: Enterovirus uncoating receptors bind at the surface depression ("canyon") that encircles each capsid vertex causing the release of a host-derived lipid called "pocket factor" that is buried in a ...Enterovirus uncoating receptors bind at the surface depression ("canyon") that encircles each capsid vertex causing the release of a host-derived lipid called "pocket factor" that is buried in a hydrophobic pocket formed by the major viral capsid protein, VP1. Coxsackievirus and adenovirus receptor (CAR) is a universal uncoating receptor of group B coxsackieviruses (CVB). Here, we present five high-resolution cryoEM structures of CVB representing different stages of virus infection. Structural comparisons show that the CAR penetrates deeper into the canyon than other uncoating receptors, leading to a cascade of events: collapse of the VP1 hydrophobic pocket, high-efficiency release of the pocket factor and viral uncoating and genome release under neutral pH, as compared with low pH. Furthermore, we identified a potent therapeutic antibody that can neutralize viral infection by interfering with virion-CAR interactions, destabilizing the capsid and inducing virion disruption. Together, these results define the structural basis of CVB cell entry and antibody neutralization. | |||||||||
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 | ![]() | 103.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.1 KB 13.1 KB | Display Display | ![]() |
Images | ![]() | 215.1 KB | ||
Filedesc metadata | ![]() | 5.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dpfMC ![]() 7dpgC ![]() 7dpzC ![]() 7dq1C ![]() 7dq4C ![]() 7dq7C 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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Annotation | Cryo-EM structure of Coxsackievirus B1 mature virion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.128 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 B1
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Coxsackievirus B1
Supramolecule | Name: Coxsackievirus B1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / NCBI-ID: 12071 / Sci species name: Coxsackievirus B1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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-Macromolecule #1: Virion protein 1
Macromolecule | Name: Virion protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 31.207117 KDa |
Sequence | String: GPVEESVDRA VARVADTISS RPTNSESIPA LTAAETGHTS QVVPSDTMQT RHVKNYHSRS ESSIENFLCR SACVYYATYT NNSKKGFAE WVINTRQVAQ LRRKLELFTY LRFDLELTFV ITSAQQPSTA SSVDAPVQTH QIMYVPPGGP VPTKVKDYAW Q TSTNPSVF ...String: GPVEESVDRA VARVADTISS RPTNSESIPA LTAAETGHTS QVVPSDTMQT RHVKNYHSRS ESSIENFLCR SACVYYATYT NNSKKGFAE WVINTRQVAQ LRRKLELFTY LRFDLELTFV ITSAQQPSTA SSVDAPVQTH QIMYVPPGGP VPTKVKDYAW Q TSTNPSVF WTEGNAPPRM SIPFISIGNA YSCFYDGWTQ FSRNGVYGIN TLNNMGTLYM RHVNEAGQGP IKSTVRIYFK PK HVKAWVP RPPRLCQYEK QKNVNFSPIG VTTSRTDIIT T 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: 29.122744 KDa |
Sequence | String: SPSAEECGYS DRVRSITLGN STITTQECAN VVVGYGVWPE YLKDNEATAE DQPTQPDVAT CRFYTLESVQ WMKNSAGWWW KLPDALSQM GLFGQNMQYH YLGRTGYTIH VQCNASKFHQ GCLLVVCVPE AEMGCSNLNN TPEFSELSGG DSARMFTDTQ V GESNAKKV ...String: SPSAEECGYS DRVRSITLGN STITTQECAN VVVGYGVWPE YLKDNEATAE DQPTQPDVAT CRFYTLESVQ WMKNSAGWWW KLPDALSQM GLFGQNMQYH YLGRTGYTIH VQCNASKFHQ GCLLVVCVPE AEMGCSNLNN TPEFSELSGG DSARMFTDTQ V GESNAKKV QTAVWNAGMG VGVGNLTIFP HQWINLRTNN SATLVMPYIN SVPMDNMFRH NNLTLMIIPF VPLNYSEGSS PY VPITVTI APMCAEYNGL RLASNQ 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: 26.328764 KDa |
Sequence | String: GLPVMTTPGS TQFLTSDDFQ SPSAMPQFDV TPEMQIPGRV NNLMEIAEVD SVVPVNNTED NVSSLKAYQI PVQSNSDNGK QVFGFPLQP GANNVLNRTL LGEILNYYTH WSGSIKLTFM FCGSAMATGK FLLAYSPPGA GVPKNRKDAM LGTHVIWDVG L QSSCVLCV ...String: GLPVMTTPGS TQFLTSDDFQ SPSAMPQFDV TPEMQIPGRV NNLMEIAEVD SVVPVNNTED NVSSLKAYQI PVQSNSDNGK QVFGFPLQP GANNVLNRTL LGEILNYYTH WSGSIKLTFM FCGSAMATGK FLLAYSPPGA GVPKNRKDAM LGTHVIWDVG L QSSCVLCV PWISQTHYRY VVEDEYTAAG YVTCWYQTNI VVPADVQSSC DILCFVSACN DFSVRMLKDT PFIRQDTFYQ UniProtKB: Genome polyprotein |
-Macromolecule #4: Capsid protein VP4
Macromolecule | Name: Capsid protein VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 7.484246 KDa |
Sequence | String: MGAQVSTQKT GAHETGLNAS GNSVIHYTNI NYYKDAASNS ANRQDFTQDP GKFTEPVKDI MVKTMPALN UniProtKB: Genome polyprotein |
-Macromolecule #5: PALMITIC ACID
Macromolecule | Name: PALMITIC ACID / type: ligand / ID: 5 / Number of copies: 1 / Formula: PLM |
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Molecular weight | Theoretical: 256.424 Da |
Chemical component information | ![]() ChemComp-PLM: |
-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 TECNAI F30 |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / 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: Tecnai F30 / 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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 35999 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |