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- EMDB-31556: Complex of FMDV A/AF/72 and bovine neutralizing scFv antibody R55 -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-31556 | |||||||||
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Title | Complex of FMDV A/AF/72 and bovine neutralizing scFv antibody R55 | |||||||||
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Function / homology | ![]() L-peptidase / modulation by virus of host chromatin organization / RNA-protein covalent cross-linking / : / : / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane ...L-peptidase / modulation by virus of host chromatin organization / RNA-protein covalent cross-linking / : / : / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / regulation of translation / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / RNA binding / ATP binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.91 Å | |||||||||
![]() | He Y / Li K / Lou Z | |||||||||
![]() | ![]() Title: Structures of Foot-and-Mouth Disease Virus with Bovine Neutralizing Antibodies Reveal the Determinant of Intraserotype Cross-Neutralization. Authors: Yong He / Kun Li / Li Wang / Zixian Sun / Yimei Cao / Pinghua Li / Pu Sun / Huifang Bao / Shasha Zhou / Sheng Wang / Xingwen Bai / Xuerong Liu / Lixia Zhao / Xiuli Fan / Zaixin Liu / Zengjun ...Authors: Yong He / Kun Li / Li Wang / Zixian Sun / Yimei Cao / Pinghua Li / Pu Sun / Huifang Bao / Shasha Zhou / Sheng Wang / Xingwen Bai / Xuerong Liu / Lixia Zhao / Xiuli Fan / Zaixin Liu / Zengjun Lu / Cheng Yang / Zhiyong Lou / ![]() Abstract: Foot-and-mouth disease virus (FMDV) exhibits broad antigenic diversity with poor intraserotype cross-neutralizing activity. Studies of the determinant involved in this diversity are essential for the ...Foot-and-mouth disease virus (FMDV) exhibits broad antigenic diversity with poor intraserotype cross-neutralizing activity. Studies of the determinant involved in this diversity are essential for the development of broadly protective vaccines. In this work, we isolated a bovine antibody, designated R55, that displays cross-reaction with both FMDV A/AF/72 (hereafter named FMDV-AAF) and FMDV A/WH/09 (hereafter named FMDV-AWH) but only has a neutralizing effect on FMDV-AWH. Near-atomic resolution structures of FMDV-AAF-R55 and FMDV-AWH-R55 show that R55 engages the capsids of both FMDV-AAF and FMDV-AWH near the icosahedral 3-fold axis and binds to the βB and BC/HI-loops of VP2 and to the B-B knob of VP3. The common interaction residues are highly conserved, which is the major determinant for cross-reaction with both FMDV-AAF and FMDV-AWH. In addition, the cryo-EM structure of the FMDV-AWH-R55 complex also shows that R55 binds to E70 located at the VP3 BC-loop in an adjacent pentamer, which enhances the acid and thermal stabilities of the viral capsid. This may prevent capsid dissociation and genome release into host cells, eventually leading to neutralization of the viral infection. In contrast, R55 binds only to the FMDV-AAF capsid within one pentamer due to the E70G variation, which neither enhances capsid stability nor neutralizes FMDV-AAF infection. The E70G mutation is the major determinant involved in the neutralizing differences between FMDV-AWH and FMDV-AAF. The crucial amino acid E70 is a key component of the neutralizing epitopes, which may aid in the development of broadly protective vaccines. Foot-and-mouth disease virus (FMDV) causes a highly contagious and economically devastating disease in cloven-hoofed animals, and neutralizing antibodies play critical roles in the defense against viral infections. Here, we isolated a bovine antibody (R55) using the single B cell antibody isolation technique. Enzyme-linked immunosorbent assays (ELISA) and virus neutralization tests (VNT) showed that R55 displays cross-reactions with both FMDV-AWH and FMDV-AAF but only has a neutralizing effect on FMDV-AWH. Cryo-EM structures, fluorescence-based thermal stability assays and acid stability assays showed that R55 engages the capsid of FMDV-AWH near the icosahedral 3-fold axis and informs an interpentamer epitope, which overstabilizes virions to hinder capsid dissociation to release the genome, eventually leading to neutralization of viral infection. The crucial amino acid E70 forms a key component of neutralizing epitopes, and the determination of the E70G mutation involved in the neutralizing differences between FMDV-AWH and FMDV-AAF could aid in the development of broadly protective vaccines. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 97.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.7 KB 15.7 KB | Display Display | ![]() |
Images | ![]() | 247 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7fejMC ![]() 7feiC 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: 0.93 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 : Complex of FMDV A/AF/72 and bovine neutralizing scFv antibody R55
Entire | Name: Complex of FMDV A/AF/72 and bovine neutralizing scFv antibody R55 |
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Components |
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-Supramolecule #1: Complex of FMDV A/AF/72 and bovine neutralizing scFv antibody R55
Supramolecule | Name: Complex of FMDV A/AF/72 and bovine neutralizing scFv antibody R55 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #2: FMDV A/AF/72
Supramolecule | Name: FMDV A/AF/72 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: and bovine neutralizing scFv antibody R55
Supramolecule | Name: and bovine neutralizing scFv antibody R55 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6 |
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-Macromolecule #1: A/AF/72 VP1
Macromolecule | Name: A/AF/72 VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 23.417545 KDa |
Sequence | String: TTTTGESADP VTTTVENYGG ETQVQRRQHT NVGFIMDRFV KIPSQSPTHV IDLMQTHQHG LVGALLRAAT YYFSDLEIVV RHDDNLTWV PNGAPETALH NTSNPTAYRK GPFTRLALPY TAPHRVLATV YNGTTKYSTG NAGRRGDLGS LAARVAAQLP A SFNFGAIR ...String: TTTTGESADP VTTTVENYGG ETQVQRRQHT NVGFIMDRFV KIPSQSPTHV IDLMQTHQHG LVGALLRAAT YYFSDLEIVV RHDDNLTWV PNGAPETALH NTSNPTAYRK GPFTRLALPY TAPHRVLATV YNGTTKYSTG NAGRRGDLGS LAARVAAQLP A SFNFGAIR ATVIHELLVR MKRAELYCPR PLLAVEVTSQ DRHKQRIIAP AKQL |
-Macromolecule #2: A/AF/72 VP2
Macromolecule | Name: A/AF/72 VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 24.561641 KDa |
Sequence | String: DKKTEETTLL EDRILTTRNG HTTSTTQSSV GVTYGYSTGE DHVSGPNTSG LETRVTQAER FFKKHLFDWT TDKAFGHLEK LELPTDHKG VYGHLVDSFA YMRNGWDVEV SAVGNQFNGG CLLVAMVPEY KDFTLREKYQ LTLFPHQFIS PRTNMTAHIT V PYLGVNRY ...String: DKKTEETTLL EDRILTTRNG HTTSTTQSSV GVTYGYSTGE DHVSGPNTSG LETRVTQAER FFKKHLFDWT TDKAFGHLEK LELPTDHKG VYGHLVDSFA YMRNGWDVEV SAVGNQFNGG CLLVAMVPEY KDFTLREKYQ LTLFPHQFIS PRTNMTAHIT V PYLGVNRY DQYKKHKPWT LVVMVLSPLT VNNSGAGQIK VYANIAPTYV HVAGELPSKE |
-Macromolecule #3: A/AF/72 VP3
Macromolecule | Name: A/AF/72 VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 24.142053 KDa |
Sequence | String: GIVPVACSAG YGGLVTTDPK TADPIYGMVY NPPRTNYPGR FTNLLDVAEA CPTFLCFDDG KPYVVTRADG QRLLAKFDVS LAAKHMSNT YLSGIAQYYA QYSGTINLHF MFTGPTDSKA RYMVAYVPPG METPPDTPEE AAHCIHAEWD TGLNSKFTFS I PYVSAADY ...String: GIVPVACSAG YGGLVTTDPK TADPIYGMVY NPPRTNYPGR FTNLLDVAEA CPTFLCFDDG KPYVVTRADG QRLLAKFDVS LAAKHMSNT YLSGIAQYYA QYSGTINLHF MFTGPTDSKA RYMVAYVPPG METPPDTPEE AAHCIHAEWD TGLNSKFTFS I PYVSAADY AYTASDVAET TNVQGWVCIY QITHGKAEDD TLVVSLSAGK DFELRLPIDP RSQ |
-Macromolecule #4: Capsid protein VP0
Macromolecule | Name: Capsid protein VP0 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase |
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Source (natural) | Organism: Foot-and-mouth disease virus |
Molecular weight | Theoretical: 8.805154 KDa |
Sequence | String: GAGQSSPATG SQNQSGNTGS IINNYYMQQY QNSMDTQLGD NAISGGSNEG STDTTSTHTN NTQNNDWFSK LASSAFTGLF 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: ![]() ![]() |
Molecular weight | Theoretical: 13.615155 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: QVQLRESGPS LVKPSQTLSL TCTVSGFSLS DYAVGWVRQA PGKALEFLGS ISTGGNTGYN PALKSRLSIT KDNSKNQVSL SLSSVTTED TATYYCTKSI HSYSVFEYTY MQYVDAWGQG LLVPVSS |
-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: ![]() ![]() |
Molecular weight | Theoretical: 12.88685 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: WAQAVLTQPS SVSGSLGQRV SITCSGSSNN IGRYDVGWYQ QIPGSGLRTI IYASKNRPSG VPDRFSGSRS GNTATLTISS LQAEDEADY FCATGDYSSS TSVFGSGTTL TVLGDYKDDD DKGG |
-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 ARCTICA |
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Image recording | Film or detector model: DIRECT ELECTRON DE-16 (4k x 4k) / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 25317 |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |