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Yorodumi- EMDB-31223: FOOT AND MOUTH DISEASE VIRUS O/TIBET/99-BOUND THE SINGLE CHAIN FR... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31223 | |||||||||
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Title | FOOT AND MOUTH DISEASE VIRUS O/TIBET/99-BOUND THE SINGLE CHAIN FRAGMEN ANTIBODY C4 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | FOOT AND MOUTH DISEASE VIRUS / FMDV / VIRUS | |||||||||
Function / homology | Function and homology information Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold Similarity search - Domain/homology | |||||||||
Biological species | Foot-and-mouth disease virus / Bos taurus (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.75 Å | |||||||||
Authors | He Y / Li K | |||||||||
Citation | Journal: J Virol / Year: 2021 Title: Two Cross-Protective Antigen Sites on Foot-and-Mouth Disease Virus Serotype O Structurally Revealed by Broadly Neutralizing Antibodies from Cattle. Authors: Kun Li / Yong He / Li Wang / Pinghua Li / Sheng Wang / Pu Sun / Huifang Bao / Yimei Cao / Xuerong Liu / Guoqiang Zhu / Yali Song / Xingwen Bai / Xueqing Ma / Yuanfang Fu / Hong Yuan / Jing ...Authors: Kun Li / Yong He / Li Wang / Pinghua Li / Sheng Wang / Pu Sun / Huifang Bao / Yimei Cao / Xuerong Liu / Guoqiang Zhu / Yali Song / Xingwen Bai / Xueqing Ma / Yuanfang Fu / Hong Yuan / Jing Zhang / Jian Wang / Yingli Chen / Dong Li / Zhiyong Lou / Zaixin Liu / Zengjun Lu / Abstract: Foot-and-mouth disease virus (FMDV) is a highly contagious virus that infects cloven-hoofed animals. Neutralizing antibodies play critical roles in antiviral infection. Although five known antigen ...Foot-and-mouth disease virus (FMDV) is a highly contagious virus that infects cloven-hoofed animals. Neutralizing antibodies play critical roles in antiviral infection. Although five known antigen sites that induce neutralizing antibodies have been defined, studies on cross-protective antigen sites are still scarce. We mapped two cross-protective antigen sites using 13 bovine-derived broadly neutralizing monoclonal antibodies (bnAbs) capable of neutralizing 4 lineages within 3 topotypes of FMDV serotype O. One antigen site was formed by a novel cluster of VP3-focused epitopes recognized by bnAb C4 and C4-like antibodies. The cryo-electron microscopy (cryo-EM) structure of the FMDV-OTi (O/Tibet/99)-C4 complex showed close contact with VP3 and a novel interprotomer antigen epitope around the icosahedral 3-fold axis of the FMDV particle, which is far beyond the known antigen site 4. The key determinants of the neutralizing function of C4 and C4-like antibodies on the capsid were βB (T65), the B-C loop (T68), the E-F loop (E131 and K134), and the H-I loop (G196), revealing a novel antigen site on VP3. The other antigen site comprised two group epitopes on VP2 recognized by 9 bnAbs (B57, B73, B77, B82, F28, F145, F150, E46, and E54), which belong to the known antigen site 2 of FMDV serotype O. Notably, bnAb C4 potently promoted FMDV RNA release in response to damage to viral particles, suggesting that the targeted epitope contains a trigger mechanism for particle disassembly. This study revealed two cross-protective antigen sites that can elicit cross-reactive neutralizing antibodies in cattle and provided new structural information for the design of a broad-spectrum molecular vaccine against FMDV serotype O. FMDV is the causative agent of foot-and-mouth disease (FMD), which is one of the most contagious and economically devastating diseases of domestic animals. The antigenic structure of FMDV serotype O is rather complicated, especially for those sites that can elicit a cross-protective neutralizing antibody response. Monoclonal neutralization antibodies provide both crucial defense components against FMDV infection and valuable tools for fine analysis of the antigenic structure. In this study, we found a cluster of novel VP3-focused epitopes using 13 bnAbs against FMDV serotype O from natural host cattle, which revealed two cross-protective antigen sites on VP2 and VP3. Antibody C4 targeting this novel epitope potently promoted viral particle disassembly and RNA release before infection, which may indicate a vulnerable region of FMDV. This study reveals new structural information about cross-protective antigen sites of FMDV serotype O, providing valuable and strong support for future research on broad-spectrum vaccines against FMD. | |||||||||
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_31223.map.gz | 96.6 MB | EMDB map data format | |
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Header (meta data) | emd-31223-v30.xml emd-31223.xml | 15.7 KB 15.7 KB | Display Display | EMDB header |
Images | emd_31223.png | 284.7 KB | ||
Filedesc metadata | emd-31223.cif.gz | 5.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31223 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31223 | HTTPS FTP |
-Validation report
Summary document | emd_31223_validation.pdf.gz | 542.7 KB | Display | EMDB validaton report |
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Full document | emd_31223_full_validation.pdf.gz | 542.3 KB | Display | |
Data in XML | emd_31223_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | emd_31223_validation.cif.gz | 8.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31223 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31223 | HTTPS FTP |
-Related structure data
Related structure data | 7eo0MC 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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-Map
File | Download / File: emd_31223.map.gz / Format: CCP4 / Size: 421.9 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: 0.93 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 : FMDV-OTi-C4
Entire | Name: FMDV-OTi-C4 |
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Components |
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-Supramolecule #1: FMDV-OTi-C4
Supramolecule | Name: FMDV-OTi-C4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: FOOT AND MOUTH DISEASE VIRUS O/TIBET/99
Supramolecule | Name: FOOT AND MOUTH DISEASE VIRUS O/TIBET/99 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Foot-and-mouth disease virus |
-Supramolecule #3: C4 scFv
Supramolecule | Name: C4 scFv / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6 |
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Source (natural) | Organism: Bos taurus (cattle) |
-Macromolecule #1: O/TIBET/99 VP1
Macromolecule | Name: O/TIBET/99 VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Foot-and-mouth disease virus |
Molecular weight | Theoretical: 23.524781 KDa |
Sequence | String: TTSTGESADP VTATVENYGG ETQVQRRQHT DVSFILDRFV KVTPKDQINV LDLMQTPAHT LVGALLRTAT YYFADLEVAV KHEGNLTWV PNGAPETALD NTTNPTAYHK APLTRLALPY TAPHRVLATV YNGNCKYGES PVTNARGDLQ VLAQKAARAL P TSFNYGAI ...String: TTSTGESADP VTATVENYGG ETQVQRRQHT DVSFILDRFV KVTPKDQINV LDLMQTPAHT LVGALLRTAT YYFADLEVAV KHEGNLTWV PNGAPETALD NTTNPTAYHK APLTRLALPY TAPHRVLATV YNGNCKYGES PVTNARGDLQ VLAQKAARAL P TSFNYGAI KATRVTELLY RMKRAETYCP RPLLAIHPSE ARHKQKIVAP VKQLL |
-Macromolecule #2: O/TIBET/99 VP2
Macromolecule | Name: O/TIBET/99 VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Foot-and-mouth disease virus |
Molecular weight | Theoretical: 24.338387 KDa |
Sequence | String: DKKTEETTLL EDRILTTRNG HTTSTTQSSV GVTYGYATAE DFVSGPNTSG LETRVVQAER FFKTHLFDWV TSDPFGRCYQ LELPTDHKG VYGSLTDSYA YMRNGWDVEV TAVGNQFNGG CLLVAMVPEL CSIDKRGLYQ LTLFPHQFIN PRTNMTAHIT V PFVGVNRY ...String: DKKTEETTLL EDRILTTRNG HTTSTTQSSV GVTYGYATAE DFVSGPNTSG LETRVVQAER FFKTHLFDWV TSDPFGRCYQ LELPTDHKG VYGSLTDSYA YMRNGWDVEV TAVGNQFNGG CLLVAMVPEL CSIDKRGLYQ LTLFPHQFIN PRTNMTAHIT V PFVGVNRY DQYKVHKPWT LVVMVVAPLT VNTEGAPQIK VYANIAPTNV HVAGEFPSKE |
-Macromolecule #3: O/TIBET/99 VP3
Macromolecule | Name: O/TIBET/99 VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Foot-and-mouth disease virus |
Molecular weight | Theoretical: 23.875801 KDa |
Sequence | String: GIFPVACSDG YGGLVTTDPK TADPAYGKVF NPPRNMLPGR FTNFLDVAEA CPTFLHFEGD VPYVTTKTDS DRVLAQFDLS LAAKHMSNT FLAGLAQYYT QYSGTINLHF MFTGPTDAKA RYMIAYAPPG MEPPKTPEAA AHCIHAEWDT GLNSKFTFSI P YLSAADYA ...String: GIFPVACSDG YGGLVTTDPK TADPAYGKVF NPPRNMLPGR FTNFLDVAEA CPTFLHFEGD VPYVTTKTDS DRVLAQFDLS LAAKHMSNT FLAGLAQYYT QYSGTINLHF MFTGPTDAKA RYMIAYAPPG MEPPKTPEAA AHCIHAEWDT GLNSKFTFSI P YLSAADYA YTASDAAETT NVQGWVCLFQ ITHGKADGDA LVVLASAGKD FELRLPVDAR TQ |
-Macromolecule #4: O/TIBET/99 VP4
Macromolecule | Name: O/TIBET/99 VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Foot-and-mouth disease virus |
Molecular weight | Theoretical: 8.778129 KDa |
Sequence | String: GAGQSSPATG SQNQSGNTGS IINNYYMQQY QNSMDTQLGD NAISGGSNEG STDTTSTHTT NTQNNDWFSK LASSAFSGLF GALLA |
-Macromolecule #5: Ig heavy chain variable region
Macromolecule | Name: Ig heavy chain variable region / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Bos taurus (cattle) |
Molecular weight | Theoretical: 13.914535 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
Sequence | String: QVQLRESGPS LVKPSQTLFL TCTVSGFSLT SYSVNWVRQT PGKMLECLGG IATSGSTGYN PVLKSRLRIT KDNSKSQVSL SVSNVTPED TATYYCAKWS SRGGYDCGVH SSDYSYLDAW GQGLLVTVSS UniProtKB: Ig heavy chain variable region |
-Macromolecule #6: Ig lamda chain variable region
Macromolecule | Name: Ig lamda chain variable region / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Bos taurus (cattle) |
Molecular weight | Theoretical: 12.79488 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
Sequence | String: WAQAVLTQPS SVSASLGQRV SITCSGSSSN IGRYGATWYQ QVPGSGLRTI IYGSSRRPSG VPDRFSGSKS GNTVTLTISS LQPEDEADY FCAAYDISTN AVFGSGTTLT LLGDYKDDDD KGG UniProtKB: Ig lamda chain variable region |
-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 TALOS ARCTICA |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: OTHER |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14458 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |