+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34234 | |||||||||
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Title | Echovirus3 empty particle in complex with 6D10 Fab (sideling) | |||||||||
Map data | ||||||||||
Sample |
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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 / channel activity / protein complex oligomerization / 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 / channel activity / protein complex oligomerization / cytoplasmic vesicle membrane / monoatomic ion channel activity / endocytosis involved in viral entry into host cell / monoatomic ion transmembrane transport / nucleoside-triphosphate phosphatase / DNA replication / 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 Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) / Echovirus E3 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Wang X / Fu W | |||||||||
Funding support | 1 items
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Citation | Journal: Viruses / Year: 2022 Title: Structural Basis for the Immunogenicity of the C-Terminus of VP1 of Echovirus 3 Revealed by the Binding of a Neutralizing Antibody. Authors: Shuai Qi / Wangjun Fu / Jinyan Fan / Li Zhang / Binyang Zheng / Kang Wang / Xiangxi Wang / Ling Zhu / Xinjian Li / Yuxia Zhang / Abstract: Echovirus 3 (E3), a serotype of human enterovirus B (HEV-B), causes severe diseases in infants. Here, we determined the structures of E3 with a monoclonal antibody (MAb) 6D10 by cryo-EM to ...Echovirus 3 (E3), a serotype of human enterovirus B (HEV-B), causes severe diseases in infants. Here, we determined the structures of E3 with a monoclonal antibody (MAb) 6D10 by cryo-EM to comprehensively understand the specificities and the immunological characteristic of this serotype. The solved cryo-EM structures of the F-, A-, and E-particles of E3 bound with 6D10 revealed the structural features of the virus-antibody interface. Importantly, the structures of E-particles bound with 6D10 revealed for the first time the nature of the C-terminus of VP1 for HEV-Bs at the structural level. The highly immunogenic nature of this region in the E-particles provides new strategies for vaccine development for HEV-Bs. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34234.map.gz | 196.5 MB | EMDB map data format | |
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Header (meta data) | emd-34234-v30.xml emd-34234.xml | 18.8 KB 18.8 KB | Display Display | EMDB header |
Images | emd_34234.png | 61.6 KB | ||
Others | emd_34234_half_map_1.map.gz emd_34234_half_map_2.map.gz | 166 MB 166 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34234 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34234 | HTTPS FTP |
-Validation report
Summary document | emd_34234_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_34234_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_34234_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | emd_34234_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34234 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34234 | HTTPS FTP |
-Related structure data
Related structure data | 8gsfMC 8gscC 8gsdC 8gseC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_34234.map.gz / Format: CCP4 / Size: 209.3 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:
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-Supplemental data
-Half map: #2
File | emd_34234_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34234_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Echovirus3 empty particle in complex with 6D10 Fab (sideling)
Entire | Name: Echovirus3 empty particle in complex with 6D10 Fab (sideling) |
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Components |
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-Supramolecule #1: Echovirus3 empty particle in complex with 6D10 Fab (sideling)
Supramolecule | Name: Echovirus3 empty particle in complex with 6D10 Fab (sideling) type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #3: 6D10 Fab
Supramolecule | Name: 6D10 Fab / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #4-#5 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Supramolecule #2: Echovirus E3
Supramolecule | Name: Echovirus E3 / type: virus / ID: 2 / Parent: 1 / Macromolecule list: #1-#3 / NCBI-ID: 47516 / Sci species name: Echovirus E3 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: Yes |
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-Macromolecule #1: VP1
Macromolecule | Name: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Echovirus E3 |
Molecular weight | Theoretical: 26.940322 KDa |
Sequence | String: YHSRTESSIE NFLCRAACVY IATYASAGGT PTERYASWRI NTRQMVQLRR KFELFTYLRF DMEITFVITS TQDPGTQLAQ DMPVLTHQI MYIPPGGPVP NSATDFAWQS STNPSIFWTE GCAPARMSVP FISIGNAYSN FYDGWSHFTQ EGVYGFNSLN N MGHIYVRH ...String: YHSRTESSIE NFLCRAACVY IATYASAGGT PTERYASWRI NTRQMVQLRR KFELFTYLRF DMEITFVITS TQDPGTQLAQ DMPVLTHQI MYIPPGGPVP NSATDFAWQS STNPSIFWTE GCAPARMSVP FISIGNAYSN FYDGWSHFTQ EGVYGFNSLN N MGHIYVRH VNEQSLGVST STLRVYFKPK HVRAWVPRPP RLSPYVKSSN VNFKPTAVTT ERKDINDVGT LRPVGYTNH |
-Macromolecule #2: VP0
Macromolecule | Name: VP0 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Echovirus E3 |
Molecular weight | Theoretical: 28.069537 KDa |
Sequence | String: RVRSITLGNS TITTQECANV VVGYGVWPSY LQDNEATAED QPTQPDVATC RFYTLDSIQW QKESDGWWWK FPEALKNMGL FGQNMEYHY LGRSGYTIHV QCNASKFHQG CLLVVCVPEA EMGCSDVERE VVAASLSSED TAKSFSRTES NGQHTVQTVV Y NAGMGVGV ...String: RVRSITLGNS TITTQECANV VVGYGVWPSY LQDNEATAED QPTQPDVATC RFYTLDSIQW QKESDGWWWK FPEALKNMGL FGQNMEYHY LGRSGYTIHV QCNASKFHQG CLLVVCVPEA EMGCSDVERE VVAASLSSED TAKSFSRTES NGQHTVQTVV Y NAGMGVGV GNLTIFPHQW INLRTNNSAT IVMPYINSVP MDNMFRHYNF TLMIIPFAKL EYTEQASNYV PITVTVAPMC AE YNGLRLA SHQ |
-Macromolecule #3: VP3
Macromolecule | Name: VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Echovirus E3 |
Molecular weight | Theoretical: 25.896449 KDa |
Sequence | String: MLTPGSNQFL TSDDFQSPSA MPQFDVTPEM KIPGEVHNLM EIAEVDSVVP VNNTKENINS MEAYRIPVTG GDQLHTQVFG FQMQPGLNS VFKRTLLGEI LNYYAHWSGS VKLTFVFCGS AMATGKFLLA YSPPGASPPQ NRKQAMLGTH VIWDVGLQSS C VLCIPWIS ...String: MLTPGSNQFL TSDDFQSPSA MPQFDVTPEM KIPGEVHNLM EIAEVDSVVP VNNTKENINS MEAYRIPVTG GDQLHTQVFG FQMQPGLNS VFKRTLLGEI LNYYAHWSGS VKLTFVFCGS AMATGKFLLA YSPPGASPPQ NRKQAMLGTH VIWDVGLQSS C VLCIPWIS QTHYRLVQQD EYTSAGYVTC WYQTGLIVPP GAPPSCTILC FASACNDFSV RNLRDTPFIE QTQLLQ |
-Macromolecule #4: Heavy chain of 6D10
Macromolecule | Name: Heavy chain of 6D10 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 12.9382 KDa |
Recombinant expression | Organism: Mus musculus (house mouse) |
Sequence | String: EVQLQQSGPE LARPWASVKI SCQAFYTFSN YGMQWVKQSP GQGLEWIGPF YPGNADTSYN QKFKGKATLT ADKSSSTAYM QFSSLTSED SAVYYCARVV ATTDFDYWGQ GTTVTVSS |
-Macromolecule #5: Light chain of 6D10
Macromolecule | Name: Light chain of 6D10 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 12.652158 KDa |
Recombinant expression | Organism: Mus musculus (house mouse) |
Sequence | String: YIEASQSPSS LAVSVGEKVT MSCKSSQSLL YSSNQKNYLA WFQQKPGQSP KLLIYWASTR ESGVPDRFTG SGSGTDFTLT ISSVKAEDL AVYYCQQYYS YPYTFGGGTK LKIKR |
-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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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 30.0 e/Å2 |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22712 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |