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Yorodumi- EMDB-30565: FOOT AND MOUTH DISEASE VIRUS A/WH/CHA/09-BOUND THE SINGLE CHAIN F... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30565 | |||||||||
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Title | FOOT AND MOUTH DISEASE VIRUS A/WH/CHA/09-BOUND THE SINGLE CHAIN FRAGME ANTIBODY R50 | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Foot-and-mouth disease virus / Bos taurus (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.49 Å | |||||||||
Authors | He Y / Lou Z | |||||||||
Citation | Journal: PLoS Pathog / Year: 2021 Title: Structures of Foot-and-mouth Disease Virus with neutralizing antibodies derived from recovered natural host reveal a mechanism for cross-serotype neutralization. Authors: Yong He / Kun Li / Yimei Cao / Zixian Sun / Pinghua Li / Huifang Bao / Sheng Wang / Guoqiang Zhu / Xingwen Bai / Pu Sun / Xuerong Liu / Cheng Yang / Zaixin Liu / Zengjun Lu / Zihe Rao / Zhiyong Lou / Abstract: The development of a universal vaccine against foot-and-mouth disease virus (FMDV) is hindered by cross-serotype antigenic diversity and by a lack of knowledge regarding neutralization of the virus ...The development of a universal vaccine against foot-and-mouth disease virus (FMDV) is hindered by cross-serotype antigenic diversity and by a lack of knowledge regarding neutralization of the virus in natural hosts. In this study, we isolated serotype O-specific neutralizing antibodies (NAbs) (F145 and B77) from recovered natural bovine hosts by using the single B cell antibody isolation technique. We also identified a serotype O/A cross-reacting NAb (R50) and determined virus-NAb complex structures by cryo-electron microscopy at near-atomic resolution. F145 and B77 were shown to engage the capsid of FMDV-O near the icosahedral threefold axis, binding to the BC/HI-loop of VP2. In contrast, R50 engages the capsids of both FMDV-O and FMDV-A between the 2- and 5-fold axes and binds to the BC/EF/GH-loop of VP1 and to the GH-loop of VP3 from two adjacent protomers, revealing a previously unknown antigenic site. The cross-serotype neutralizing epitope recognized by R50 is highly conserved among serotype O/A. These findings help to elucidate FMDV neutralization by natural hosts and provide epitope information for the development of a universal vaccine for cross-serotype protection against FMDV. | |||||||||
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_30565.map.gz | 91.7 MB | EMDB map data format | |
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Header (meta data) | emd-30565-v30.xml emd-30565.xml | 16.7 KB 16.7 KB | Display Display | EMDB header |
Images | emd_30565.png | 312 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30565 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30565 | HTTPS FTP |
-Validation report
Summary document | emd_30565_validation.pdf.gz | 472.3 KB | Display | EMDB validaton report |
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Full document | emd_30565_full_validation.pdf.gz | 471.8 KB | Display | |
Data in XML | emd_30565_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | emd_30565_validation.cif.gz | 8.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30565 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30565 | HTTPS FTP |
-Related structure data
Related structure data | 7d3rMC 7d3kC 7d3lC 7d3mC 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_30565.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 : Foot-and-mouth disease virus
Entire | Name: Foot-and-mouth disease virus |
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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: Foot-and-mouth disease virus |
-Supramolecule #3: R50 VH/VL
Supramolecule | Name: R50 VH/VL / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6 Details: Single-chain fragment variable (scFv) was designed by splicing the VH and VL genes using a flexible linker (GGGGSGGGGSGGGGS). The C-termini of the scFv included a His tag. |
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Source (natural) | Organism: Bos taurus (cattle) |
-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: Foot-and-mouth disease virus |
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 |
-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: Foot-and-mouth disease virus |
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 |
-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: Foot-and-mouth disease virus |
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 |
-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: Foot-and-mouth disease virus |
Molecular weight | Theoretical: 8.778129 KDa |
Sequence | String: GAGQSSPATG SQNQSGNTGS IINNYYMQQY QNSMDTQLGD NAISGGSNEG STDTTSSHTT NTQNNDWFSK LASSAFTGLF GALLA |
-Macromolecule #5: R50 VH
Macromolecule | Name: R50 VH / 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: 18.081119 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
Sequence | String: QVQLRESGPS LVKPSQTLSL TCTASGLSLS DKAVGWVRRA PTKALEWLGS IDTGSSTGYN PGLKSRLSIT KDNSRNQVSL TITSVTTED SATYYCATVH QHTSEKRTCP RAYRPDCAAR WDCPGGADCG YCNFGAGSYG RCTPFTLTYT FENYVHTWGQ G LLVTVSS |
-Macromolecule #6: R50 VL
Macromolecule | Name: R50 VL / 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: 12.705525 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
Sequence | String: WAQAVLTQPS SVSGSLGQRV SITCSGSSSN VGNGYVSWYQ LIPGSAPRTL IYGDTNRASG VPDRFSGSRA GNTATLSISS LQAEDEAEY FCASPEDSSS NANFGSGTTL TVLGDYKDDD DKGG |
-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 TECNAI ARCTICA |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 1.63 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing #1
Image processing ID | 1 |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15460 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
-Image processing #2
Image processing ID | 2 |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15460 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-7d3r: |