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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-30321 | |||||||||
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Title | Coxsackievirus B5 (CVB5) F-particle | |||||||||
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![]() | Echovirus B / mature / VIRUS | |||||||||
Function / homology | ![]() RNA-protein covalent cross-linking / : / : / 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 ...RNA-protein covalent cross-linking / : / : / 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 / viral capsid / symbiont-mediated suppression of host gene expression / 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 / 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: 3.5 Å | |||||||||
![]() | Wang K / Rao Z | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of Echovirus 30 in complex with its receptors inform a rational prediction for enterovirus receptor usage. Authors: Kang Wang / Ling Zhu / Yao Sun / Minhao Li / Xin Zhao / Lunbiao Cui / Li Zhang / George F Gao / Weiwei Zhai / Fengcai Zhu / Zihe Rao / Xiangxi Wang / ![]() Abstract: Receptor usage that determines cell tropism and drives viral classification closely correlates with the virus structure. Enterovirus B (EV-B) consists of several subgroups according to receptor ...Receptor usage that determines cell tropism and drives viral classification closely correlates with the virus structure. Enterovirus B (EV-B) consists of several subgroups according to receptor usage, among which echovirus 30 (E30), a leading causative agent for human aseptic meningitis, utilizes FcRn as an uncoating receptor. However, receptors for many EVs remain unknown. Here we analyzed the atomic structures of E30 mature virion, empty- and A-particles, which reveals serotype-specific epitopes and striking conformational differences between the subgroups within EV-Bs. Of these, the VP1 BC loop markedly distinguishes E30 from other EV-Bs, indicative of a role as a structural marker for EV-B. By obtaining cryo-electron microscopy structures of E30 in complex with its receptor FcRn and CD55 and comparing its homologs, we deciphered the underlying molecular basis for receptor recognition. Together with experimentally derived viral receptor identifications, we developed a structure-based in silico algorithm to inform a rational prediction for EV receptor usage. | |||||||||
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 | ![]() | 166.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.3 KB 15.3 KB | Display Display | ![]() |
Images | ![]() | 135.3 KB | ||
Filedesc metadata | ![]() | 6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7c9yMC ![]() 7c9sC ![]() 7c9tC ![]() 7c9uC ![]() 7c9vC ![]() 7c9wC ![]() 7c9xC ![]() 7c9zC 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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Voxel size | X=Y=Z: 1.345 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 B5
Entire | Name: ![]() |
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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: #1-#4 Details: Particles purified from the cell cultures innoculated with the live CB5. NCBI-ID: 12074 / Sci species name: Coxsackievirus B5 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: ![]() |
Virus shell | Shell ID: 1 / Diameter: 30.0 Å / T number (triangulation number): 3 |
-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: 31.574322 KDa |
Sequence | String: GPTGEAVERA IARVADTIGS GPVNSESIPA LTAAETGHTS QVVPADTMQT RHVKNYHSRS ESTVENFLCR SACVFYTTYR NHGTDGDNF GYWVISTRQV AQLRRKLEMF TYARFDLELT FVITSTQEQS TIQGQDSPVL THQIMYVPPG GPVPTKVNSY S WQTSTNPS ...String: GPTGEAVERA IARVADTIGS GPVNSESIPA LTAAETGHTS QVVPADTMQT RHVKNYHSRS ESTVENFLCR SACVFYTTYR NHGTDGDNF GYWVISTRQV AQLRRKLEMF TYARFDLELT FVITSTQEQS TIQGQDSPVL THQIMYVPPG GPVPTKVNSY S WQTSTNPS VFWTEGSAPP RMSIPFISIG NAYSMFYDGW AKFDKQGTYG INTLNNMGTL YMRHVNDGSP GPIVSTVRIY FK PKHVKTW VPRPPRLCQY QKAGNVNFEP TGVTESRTDI TTMQTT 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: 28.626143 KDa |
Sequence | String: SPSAEECGYS DRVRSITLGN STITTQECAN VVVGYGVWPT YLNDDEATAE DQPTQPDVAT CRFYTLESVM WQQSSPGWWW KFPDALSNM GLFGQNMQYH YLGRAGYTVH VQCNASKFHQ GCLLVVCVPE AEMGCATLAN KPDQKSLSNG ETANMFESQN S TGQTAVQA ...String: SPSAEECGYS DRVRSITLGN STITTQECAN VVVGYGVWPT YLNDDEATAE DQPTQPDVAT CRFYTLESVM WQQSSPGWWW KFPDALSNM GLFGQNMQYH YLGRAGYTVH VQCNASKFHQ GCLLVVCVPE AEMGCATLAN KPDQKSLSNG ETANMFESQN S TGQTAVQA NVINAGMGVG VGNLTIFPHQ WINLRTNNSA TIVMPYINSV PMDNMFRHNN FTLMIIPFAP LSYSTGATTY VP ITVTVAP MCAEYNGLRL AGKQ |
-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: 26.163672 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 |
-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: 7.326025 KDa |
Sequence | String: GAQVSTQKTG AHETGLSASG NSIIHYTNVN YYKDAASNSA NRQDFTQDPG KFTEPVKDIM IKSMPALN |
-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: |
-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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK I |
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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) / Detector mode: SUPER-RESOLUTION / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 8890 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | ![]() PDB-7c9y: |