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Yorodumi- PDB-7fei: Complex of FMDV A/WH/CHA/09 and bovine neutralizing scFv antibody R55 -
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-Basic information
Entry | Database: PDB / ID: 7fei | ||||||
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Title | Complex of FMDV A/WH/CHA/09 and bovine neutralizing scFv antibody R55 | ||||||
Components |
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Keywords | VIRUS | ||||||
Function / homology | Function and homology information : / L-peptidase / icosahedral viral capsid / modulation by virus of host chromatin organization / positive stranded viral RNA replication / RNA-protein covalent cross-linking / : / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid ...: / L-peptidase / icosahedral viral capsid / modulation by virus of host chromatin organization / positive stranded viral RNA replication / RNA-protein covalent cross-linking / : / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / viral capsid / : / nucleoside-triphosphate phosphatase / regulation of translation / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / RNA helicase activity / viral protein processing / induction by virus of host autophagy / symbiont entry into host cell / 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 / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) Foot-and-mouth disease virus - type A | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.91 Å | ||||||
Authors | He, Y. / Li, K. / Lou, Z. | ||||||
Citation | Journal: J Virol / Year: 2021 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
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7fei.cif.gz | 162.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fei.ent.gz | 130.9 KB | Display | PDB format |
PDBx/mmJSON format | 7fei.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/7fei ftp://data.pdbj.org/pub/pdb/validation_reports/fe/7fei | HTTPS FTP |
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-Related structure data
Related structure data | 31555MC 7fejC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
-Capsid protein ... , 4 types, 4 molecules 1234
#1: Protein | Mass: 23402.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus - type A / References: UniProt: E7D639 |
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#2: Protein | Mass: 24541.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus - type A References: UniProt: J9PFK1, RNA-directed RNA polymerase, nucleoside-triphosphate phosphatase |
#3: Protein | Mass: 24157.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus - type A / References: UniProt: U5JG68 |
#4: Protein | Mass: 8778.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus - type A / References: UniProt: P03309 |
-Antibody , 2 types, 2 molecules HL
#5: Antibody | Mass: 13615.155 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli BL21 (bacteria) |
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#6: Antibody | Mass: 12886.850 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli BL21 (bacteria) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Source (natural) |
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Source (recombinant) | Organism: Escherichia coli BL21 (bacteria) | ||||||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: DIRECT ELECTRON DE-16 (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14535 / Symmetry type: POINT |