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Yorodumi- PDB-5d8a: Crystal structure of recombinant foot-and-mouth-disease virus A22... -
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-Basic information
Entry | Database: PDB / ID: 5d8a | ||||||
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Title | Crystal structure of recombinant foot-and-mouth-disease virus A22-H2093F empty capsid | ||||||
Components |
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Keywords | VIRUS / Foot and mouth disease virus / picornavirus / vaccine / aphthovirus | ||||||
Function / homology | Function and homology information modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / protein complex oligomerization / monoatomic ion channel activity / regulation of translation / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity ...modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / protein complex oligomerization / monoatomic ion channel activity / regulation of translation / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding Similarity search - Function | ||||||
Biological species | Foot-and-mouth disease virus - type A | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Kotecha, A. / Seago, J. / Scott, K. / Burman, A. / Loureiro, S. / Ren, J. / Porta, C. / Ginn, H.M. / Jackson, T. / Perez-Martin, E. ...Kotecha, A. / Seago, J. / Scott, K. / Burman, A. / Loureiro, S. / Ren, J. / Porta, C. / Ginn, H.M. / Jackson, T. / Perez-Martin, E. / Siebert, C.A. / Paul, G. / Huiskonen, J.T. / Jones, I.M. / Esnouf, R.M. / Fry, E.E. / Maree, F.F. / Charleston, B. / Stuart, D.I. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2015 Title: Structure-based energetics of protein interfaces guides foot-and-mouth disease virus vaccine design. Authors: Abhay Kotecha / Julian Seago / Katherine Scott / Alison Burman / Silvia Loureiro / Jingshan Ren / Claudine Porta / Helen M Ginn / Terry Jackson / Eva Perez-Martin / C Alistair Siebert / ...Authors: Abhay Kotecha / Julian Seago / Katherine Scott / Alison Burman / Silvia Loureiro / Jingshan Ren / Claudine Porta / Helen M Ginn / Terry Jackson / Eva Perez-Martin / C Alistair Siebert / Guntram Paul / Juha T Huiskonen / Ian M Jones / Robert M Esnouf / Elizabeth E Fry / Francois F Maree / Bryan Charleston / David I Stuart / Abstract: Virus capsids are primed for disassembly, yet capsid integrity is key to generating a protective immune response. Foot-and-mouth disease virus (FMDV) capsids comprise identical pentameric protein ...Virus capsids are primed for disassembly, yet capsid integrity is key to generating a protective immune response. Foot-and-mouth disease virus (FMDV) capsids comprise identical pentameric protein subunits held together by tenuous noncovalent interactions and are often unstable. Chemically inactivated or recombinant empty capsids, which could form the basis of future vaccines, are even less stable than live virus. Here we devised a computational method to assess the relative stability of protein-protein interfaces and used it to design improved candidate vaccines for two poorly stable, but globally important, serotypes of FMDV: O and SAT2. We used a restrained molecular dynamics strategy to rank mutations predicted to strengthen the pentamer interfaces and applied the results to produce stabilized capsids. Structural analyses and stability assays confirmed the predictions, and vaccinated animals generated improved neutralizing-antibody responses to stabilized particles compared to parental viruses and wild-type capsids. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d8a.cif.gz | 148.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d8a.ent.gz | 114.9 KB | Display | PDB format |
PDBx/mmJSON format | 5d8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d8a_validation.pdf.gz | 447.5 KB | Display | wwPDB validaton report |
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Full document | 5d8a_full_validation.pdf.gz | 451.7 KB | Display | |
Data in XML | 5d8a_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | 5d8a_validation.cif.gz | 36.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/5d8a ftp://data.pdbj.org/pub/pdb/validation_reports/d8/5d8a | HTTPS FTP |
-Related structure data
Related structure data | 3129C 3130C 5ac9C 5acaC 5ddjC 4iv1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) | ||||||||||||||||||||||||||||||||||||||||||||||||
Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 23090.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Foot-and-mouth disease virus - type A / Strain: serotype A22 Iraq / Cell line (production host): BHK-21 Clone 13 / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: Q6PN23 |
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#2: Protein | Mass: 24646.828 Da / Num. of mol.: 1 / Mutation: H93F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Foot-and-mouth disease virus - type A / Strain: serotype A22 Iraq / Cell line (production host): BHK-21, Clone 13 / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: Q6PN23 |
#3: Protein | Mass: 24245.127 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Foot-and-mouth disease virus - type A / Strain: serotype A22 Iraq / Cell line (production host): BHK-21, Clone 13 / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: Q6PN23 |
#4: Protein | Mass: 8778.129 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Foot-and-mouth disease virus - type A / Strain: serotype A22 Iraq / Cell line (production host): BHK-21, Clone 13 / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: Q6PN23 |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 4 M ammonium acetate, 100 mM bis-Tris Propane |
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-Data collection
Diffraction | Mean temperature: 298 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→50 Å / Num. obs: 356924 / % possible obs: 45.7 % / Redundancy: 1.4 % / Rmerge(I) obs: 0.265 / Χ2: 0.907 / Net I/av σ(I): 2.363 / Net I/σ(I): 2.8 / Num. measured all: 498664 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IV1 Resolution: 2.4→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0
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Solvent computation | Bsol: 40.9934 Å2 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 158.33 Å2 / Biso mean: 28.8024 Å2 / Biso min: 3.83 Å2
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Refinement step | Cycle: final / Resolution: 2.4→50 Å
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Refine LS restraints |
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Xplor file |
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