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- EMDB-34213: Complex of FMDV A/WH/CHA/09 and bovine neutralizing scFv antibody W125 -
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Open data
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Basic information
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Title | Complex of FMDV A/WH/CHA/09 and bovine neutralizing scFv antibody W125 | |||||||||
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![]() | FOOT AND MOUTH DISEASE VIRUS / FMDV / VIRUS | |||||||||
Function / homology | ![]() icosahedral viral capsid / modulation by virus of host chromatin organization / RNA-protein covalent cross-linking / : / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / viral capsid / protein complex oligomerization ...icosahedral viral capsid / modulation by virus of host chromatin organization / RNA-protein covalent cross-linking / : / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / viral capsid / protein complex oligomerization / monoatomic ion channel activity / regulation of translation / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / RNA helicase activity / viral protein processing / symbiont entry into host cell / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.72 Å | |||||||||
![]() | He Y / Kun L | |||||||||
Funding support | 1 items
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![]() | ![]() Title: Conserved antigen structures and antibody-driven variations on foot-and-mouth disease virus serotype A revealed by bovine neutralizing monoclonal antibodies. Authors: Kun Li / Yong He / Li Wang / Pinghua Li / Huifang Bao / Shulun Huang / Shasha Zhou / Guoqiang Zhu / Yali Song / Ying Li / Sheng Wang / Qianliang Zhang / Pu Sun / Xingwen Bai / Zhixun Zhao / ...Authors: Kun Li / Yong He / Li Wang / Pinghua Li / Huifang Bao / Shulun Huang / Shasha Zhou / Guoqiang Zhu / Yali Song / Ying Li / Sheng Wang / Qianliang Zhang / Pu Sun / Xingwen Bai / Zhixun Zhao / Zhiyong Lou / Yimei Cao / Zengjun Lu / Zaixin Liu / ![]() Abstract: Foot-and-mouth disease virus (FMDV) serotype A is antigenically most variable within serotypes. The structures of conserved and variable antigenic sites were not well resolved. Here, a historical ...Foot-and-mouth disease virus (FMDV) serotype A is antigenically most variable within serotypes. The structures of conserved and variable antigenic sites were not well resolved. Here, a historical A/AF72 strain from A22 lineage and a latest A/GDMM/2013 strain from G2 genotype of Sea97 lineage were respectively used as bait antigen to screen single B cell antibodies from bovine sequentially vaccinated with A/WH/CHA/09 (G1 genotype of Sea97 lineage), A/GDMM/2013 and A/AF72 antigens. Total of 39 strain-specific and 5 broad neutralizing antibodies (bnAbs) were isolated and characterized. Two conserved antigenic sites were revealed by the Cryo-EM structures of FMDV serotype A with two bnAbs W2 and W125. The contact sites with both VH and VL of W125 were closely around icosahedral threefold axis and covered the B-C, E-F, and H-I loops on VP2 and the B-B knob and H-I loop on VP3; while contact sites with only VH of W2 concentrated on B-B knob, B-C and E-F loops on VP3 scattering around the three-fold axis of viral particle. Additional highly conserved epitopes also involved key residues of VP158, VP1147 and both VP272 / VP1147 as determined respectively by bnAb W153, W145 and W151-resistant mutants. Furthermore, the epitopes recognized by 20 strain-specific neutralization antibodies involved the key residues located on VP3 68 for A/AF72 (11/20) and VP3 175 position for A/GDMM/2013 (9/19), respectively, which revealed antigenic variation between different strains of serotype A. Analysis of antibody-driven variations on capsid of two virus strains showed a relatively stable VP2 and more variable VP3 and VP1. This study provided important information on conserve and variable antigen structures to design broad-spectrum molecular vaccine against FMDV serotype A. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 95.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.9 KB 19.9 KB | Display Display | ![]() |
Images | ![]() | 260.7 KB | ||
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() | 336.6 MB 336.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 992.7 KB | Display | ![]() |
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Full document | ![]() | 992.2 KB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 21.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8grrMC ![]() 8gspC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.93 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_34213_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34213_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Foot-and-mouth disease virus
Entire | Name: ![]() ![]() |
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Components |
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-Supramolecule #1: Foot-and-mouth disease virus
Supramolecule | Name: Foot-and-mouth disease virus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: Foot-and-mouth disease virus
Supramolecule | Name: Foot-and-mouth disease virus / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: ![]() |
-Supramolecule #3: Ig chain
Supramolecule | Name: Ig chain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: A/WH/CHA/09 VP1
Macromolecule | Name: A/WH/CHA/09 VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 23.402678 KDa |
Sequence | String: TTATGESADP VTTTVENYGG ETQVQRRHHT DVSFIMDRFV QIKPVSPTHV IDLMQTHQHG LVGAMLRAAT YYFSDLEIVV NHTGRLTWV PNGAPEAALD NTSNPTAYHK APFTRLALPY TAPHRVLATV YNGNSKYSAP ATRRGDLGSL AARLAAQLPA S FNYGAIRA ...String: TTATGESADP VTTTVENYGG ETQVQRRHHT DVSFIMDRFV QIKPVSPTHV IDLMQTHQHG LVGAMLRAAT YYFSDLEIVV NHTGRLTWV PNGAPEAALD NTSNPTAYHK APFTRLALPY TAPHRVLATV YNGNSKYSAP ATRRGDLGSL AARLAAQLPA S FNYGAIRA TEIQELLVRM KRAELYCPRP LLAVKVTSQD RHKQKIIAPA KQLL UniProtKB: Genome polyprotein |
-Macromolecule #2: A/WH/CHA/09 VP2
Macromolecule | Name: A/WH/CHA/09 VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 24.541584 KDa |
Sequence | String: DKKTEETTLL EDRILTTRNG HTTSTTQSSV GVTYGYSTGE DHVSGPNTSG LETRVVQAER FFKKHLFDWT TDKPFGHIEK LELPTDHKG VYGQLVDSFA YMRNGWDVEV SAVGNQFNGG CLLVAMVPEF KEFTTREKYQ LTLFPHQFIS PRTNMTAHIT V PYLGVNRY ...String: DKKTEETTLL EDRILTTRNG HTTSTTQSSV GVTYGYSTGE DHVSGPNTSG LETRVVQAER FFKKHLFDWT TDKPFGHIEK LELPTDHKG VYGQLVDSFA YMRNGWDVEV SAVGNQFNGG CLLVAMVPEF KEFTTREKYQ LTLFPHQFIS PRTNMTAHIT V PYLGVNRY DQYNKHKPWT LVVMVVSPLT TSSIGASQIK VYTNIAPTHV HVAGELPSKE UniProtKB: Genome polyprotein |
-Macromolecule #3: A/WH/CHA/09 VP3
Macromolecule | Name: A/WH/CHA/09 VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 24.157025 KDa |
Sequence | String: GIVPVACSDG YGGLVTTDPK TADPAYGMVY NPPRTNYPGR FTNLLDVAEA CPTFLCFDDG KPYVVTRADE QRLLAKFDLS LAAKHMSNT YLSGIAQYYA QYSGTINLHF MFTGSTDSKA RYMVAYVPPG VTTPPDTPER AAHCIHAEWD TGLNSKFTFS I PYVSAADY ...String: GIVPVACSDG YGGLVTTDPK TADPAYGMVY NPPRTNYPGR FTNLLDVAEA CPTFLCFDDG KPYVVTRADE QRLLAKFDLS LAAKHMSNT YLSGIAQYYA QYSGTINLHF MFTGSTDSKA RYMVAYVPPG VTTPPDTPER AAHCIHAEWD TGLNSKFTFS I PYVSAADY AYTASDVADT TNVQGWVCIY QITHGKAEQD TLVVSVSAGK DFELRLPIDP RAQ UniProtKB: Genome polyprotein |
-Macromolecule #4: A/WH/CHA/09 VP4
Macromolecule | Name: A/WH/CHA/09 VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 8.778129 KDa |
Sequence | String: GAGQSSPATG SQNQSGNTGS IINNYYMQQY QNSMDTQLGD NAISGGSNEG STDTTSSHTT NTQNNDWFSK LASSAFTGLF GALLA UniProtKB: Genome polyprotein |
-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: 14.60416 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: QVQLRESGPS LVKPSQTLSL TCTVSGFSLS TYAVYWVRQA PGKALECLGS VSSGDYLTYN PALKSRLTIT KDNSKSEVSL SVSTVTPED TATYYCAKSH SSGYNGWIDF GCYEFTGYGP RYVDAWGQGV QVTVSS |
-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: 12.701598 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: WAQAVLTQPS SVSGSLGQRV SITCSGSSSN VGLGNYVSWF QQIPGSAPRT LIYGATNQAS GVPDRFSGSR SGNTATLTIS SLQAEDEAN YFCASPDSSQ TIFGSGTTLT VLGDYKDDDD 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: FEI FALCON II (4k x 4k) / Average electron dose: 26.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12646 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |