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Yorodumi- PDB-8grr: Complex of FMDV A/WH/CHA/09 and bovine neutralizing scFv antibody W125 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8grr | ||||||
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Title | Complex of FMDV A/WH/CHA/09 and bovine neutralizing scFv antibody W125 | ||||||
Components |
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Keywords | VIRUS / FOOT AND MOUTH DISEASE VIRUS / FMDV | ||||||
Function / homology | Function and homology information icosahedral viral capsid / symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / channel activity / viral capsid / monoatomic ion transmembrane transport / regulation of translation ...icosahedral viral capsid / symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / channel activity / viral capsid / monoatomic ion transmembrane transport / 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 | Bos taurus (cattle) Foot-and-mouth disease virus A | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.72 Å | ||||||
Authors | He, Y. / Kun, L. | ||||||
Funding support | 1items
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Citation | Journal: PLoS Pathog / Year: 2023 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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8grr.cif.gz | 166.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8grr.ent.gz | 129 KB | Display | PDB format |
PDBx/mmJSON format | 8grr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8grr_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8grr_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8grr_validation.xml.gz | 47.5 KB | Display | |
Data in CIF | 8grr_validation.cif.gz | 65.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/8grr ftp://data.pdbj.org/pub/pdb/validation_reports/gr/8grr | HTTPS FTP |
-Related structure data
Related structure data | 34213MC 8gspC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
-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 A / References: UniProt: E7D6A4 |
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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 A / References: UniProt: A0A890YS21 |
#3: Protein | Mass: 24157.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus A / References: UniProt: A0A890YS45 |
#4: Protein | Mass: 8778.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus A / References: UniProt: E9NHA3 |
-Antibody , 2 types, 2 molecules HL
#5: Antibody | Mass: 14604.160 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) / Strain (production host): BL21 |
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#6: Antibody | Mass: 12701.598 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) / Strain (production host): BL21 |
-Details
Has protein modification | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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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 TECNAI ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 26 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12646 / Symmetry type: POINT |