+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30317 | |||||||||
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Title | Echovirus 30 E-particle | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Echovirus B / premature / 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 / endocytosis involved in viral entry into host cell / cytoplasmic vesicle membrane / : ...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 / endocytosis involved in viral entry into host cell / cytoplasmic vesicle membrane / : / 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 / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Echovirus E30 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Wang K / Zhu L | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Commun / Year: 2020 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30317.map.gz | 167.1 MB | EMDB map data format | |
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Header (meta data) | emd-30317-v30.xml emd-30317.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
Images | emd_30317.png | 91.2 KB | ||
Filedesc metadata | emd-30317.cif.gz | 5.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30317 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30317 | HTTPS FTP |
-Related structure data
Related structure data | 7c9uMC 7c9sC 7c9tC 7c9vC 7c9wC 7c9xC 7c9yC 7c9zC 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_30317.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: 1.347 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 : Echovirus E30
Entire | Name: Echovirus E30 |
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Components |
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-Supramolecule #1: Echovirus E30
Supramolecule | Name: Echovirus E30 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 41846 / Sci species name: Echovirus E30 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: Homo sapiens (human) |
Virus shell | Shell ID: 1 / Diameter: 300.0 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: Echovirus E30 |
Molecular weight | Theoretical: 33.091008 KDa |
Sequence | String: NDPESALNRA VGRVADTVAS GPVNTEQIPA LTAVETGHTS QVVPSDTMQT RHVINYHTRS ESSIENFMGR AACVYIAQYA TEKVNDELD RYTNWEITTR QVAQLRRKLE MFTYMRFDLE ITFVITSSQR TSTTYASDSP PLTHQVMYVP PGGPIPKSYE D FAWQTSTN ...String: NDPESALNRA VGRVADTVAS GPVNTEQIPA LTAVETGHTS QVVPSDTMQT RHVINYHTRS ESSIENFMGR AACVYIAQYA TEKVNDELD RYTNWEITTR QVAQLRRKLE MFTYMRFDLE ITFVITSSQR TSTTYASDSP PLTHQVMYVP PGGPIPKSYE D FAWQTSTN PSVFWTEGNA PPRMSIPFMS VGNAYCNFYD GWSHFSQSGV YGYTTLNNMG HLYFRHVNKS TAYPVNSVAR VY FKPKHVK AWVPRAPRLC PYLKARNVNF NVQGVTESRN KITLDRSTHN PLANT |
-Macromolecule #2: VP0
Macromolecule | Name: VP0 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Echovirus E30 |
Molecular weight | Theoretical: 36.428777 KDa |
Sequence | String: MGAQVSTQKT GAHETGLNAS GNSIIHYTNI NYYKDSASNS LNRQDFTQDP SKFTEPVKDV MIKTLPALNS PTVEECGYSD RVRSITLGN STITTQECAN VVVGYGVWPT YLSDHEATAV DQPTQPDVAT CRFYTLESVK WESSSAGWWW KFPEALSDMG L FGQNMQYH ...String: MGAQVSTQKT GAHETGLNAS GNSIIHYTNI NYYKDSASNS LNRQDFTQDP SKFTEPVKDV MIKTLPALNS PTVEECGYSD RVRSITLGN STITTQECAN VVVGYGVWPT YLSDHEATAV DQPTQPDVAT CRFYTLESVK WESSSAGWWW KFPEALSDMG L FGQNMQYH YLGRTGYTIH VQCNASKFHQ GCLLVVCVPE AEMGAATTDH AFNHTKLSNI GQAMEFSAKK STDQTGPQTA VH NAGMGVA VGNLTIFPHQ WINLRTNNSA TIVMPYINSV PMDNMYRHYN FTLMVIPFAK LEHSPQASTY VPITVTVAPM CAE YNGLRL AGHQ |
-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: Echovirus E30 |
Molecular weight | Theoretical: 26.157531 KDa |
Sequence | String: GLPTMNTPGS TQFLTSDDFQ SPSAMPQFDV TPEIQIPGQV RNLMEIAEVD SVVPVNNTEG HVNSMEAYRI PVRPQTSSGE QVFGFQLQP GHDSVLKHTL LGEILNYYAN WSGSMKLTFM YCGAAMATGK FLIAYSPPGA GVPGSRRDAM LGTHVIWDVG L QSSCVLCV ...String: GLPTMNTPGS TQFLTSDDFQ SPSAMPQFDV TPEIQIPGQV RNLMEIAEVD SVVPVNNTEG HVNSMEAYRI PVRPQTSSGE QVFGFQLQP GHDSVLKHTL LGEILNYYAN WSGSMKLTFM YCGAAMATGK FLIAYSPPGA GVPGSRRDAM LGTHVIWDVG L QSSCVLCV PWISQTNYRY VTSDAYTDAG YITCWYQTSI VTPPDIPTTS TILCFVSACN DFSVRLLRDT PFITQQALFQ |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec. |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / 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 |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 30.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: RANDOM CONICAL TILT |
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Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 16676 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-7c9u: |