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- EMDB-30559: FOOT AND MOUTH DISEASE VIRUS O/TIBET/99-BOUND THE SINGLE CHAIN FR... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-30559 | |||||||||
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Title | FOOT AND MOUTH DISEASE VIRUS O/TIBET/99-BOUND THE SINGLE CHAIN FRAGMEN ANTIBODY F145 | |||||||||
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Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.68 Å | |||||||||
![]() | He Y / Lou Z | |||||||||
![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 114.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.2 KB 17.2 KB | Display Display | ![]() |
Images | ![]() | 297 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 491.5 KB | Display | ![]() |
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Full document | ![]() | 491.1 KB | Display | |
Data in XML | ![]() | 7.8 KB | Display | |
Data in CIF | ![]() | 8.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7d3lMC ![]() 7d3kC ![]() 7d3mC ![]() 7d3rC 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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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:
CCP4 map header:
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-Supplemental data
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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: F145 V H/L
Supramolecule | Name: F145 V H/L / 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: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-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: ![]() ![]() |
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: ![]() ![]() |
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: ![]() ![]() |
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: ![]() ![]() |
Molecular weight | Theoretical: 8.778129 KDa |
Sequence | String: GAGQSSPATG SQNQSGNTGS IINNYYMQQY QNSMDTQLGD NAISGGSNEG STDTTSTHTT NTQNNDWFSK LASSAFSGLF GALLA |
-Macromolecule #5: F145 VH
Macromolecule | Name: F145 VH / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 16.827703 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: QVQLRESGPS LVKPSQTLSL TCTASGFSLS DKAVGWVRQA PGKALEWLGS IDTGGSTGYN PGLKSRLSIT KDNSKSRVSL SVSSVTTED SATYYCTTVY HETSRTCPDG YIYDPGCGGS WVCSRLFPTD RCIVGRTTTY EWYVDAWGQG LLVTVSS |
-Macromolecule #6: F145 VL
Macromolecule | Name: F145 VL / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 12.605449 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: WAQAVLTQPS SVSGSLGQRV SITCSGSSSN VGNGYVSWYQ LIPGSAPRTL IYGDTSRASG VPDRISGSRS GNTATLTISS VQAEDEADY FCASAEDSSS NAVFGSGTTL 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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Grid | Model: Quantifoil / Material: COPPER / Mesh: 200 |
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: 1.63 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 #1
Image processing ID | 1 |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15460 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
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Image processing #2
Image processing ID | 2 |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.68 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-7d3l: |