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Yorodumi- EMDB-3749: Poliovirus type 3 (strain Saukett) stabilized virus-like particle... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3749 | |||||||||
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Title | Poliovirus type 3 (strain Saukett) stabilized virus-like particle in complex with the pocket factor compound GPP3 | |||||||||
Map data | MRC format map file. Contour level determined by visual inspection in UCSF Chimera. | |||||||||
Sample |
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Function / homology | Function and homology information symbiont genome entry into host cell via pore formation in plasma membrane / viral capsid / symbiont-mediated suppression of host gene expression / virion attachment to host cell / structural molecule activity Similarity search - Function | |||||||||
Biological species | Human poliovirus 3 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Bahar MW / Kotecha A / Fry EE / Stuart DI | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nat Commun / Year: 2017 Title: Plant-made polio type 3 stabilized VLPs-a candidate synthetic polio vaccine. Authors: Johanna Marsian / Helen Fox / Mohammad W Bahar / Abhay Kotecha / Elizabeth E Fry / David I Stuart / Andrew J Macadam / David J Rowlands / George P Lomonossoff / Abstract: Poliovirus (PV) is the causative agent of poliomyelitis, a crippling human disease known since antiquity. PV occurs in two distinct antigenic forms, D and C, of which only the D form elicits a robust ...Poliovirus (PV) is the causative agent of poliomyelitis, a crippling human disease known since antiquity. PV occurs in two distinct antigenic forms, D and C, of which only the D form elicits a robust neutralizing response. Developing a synthetically produced stabilized virus-like particle (sVLP)-based vaccine with D antigenicity, without the drawbacks of current vaccines, will be a major step towards the final eradication of poliovirus. Such a sVLP would retain the native antigenic conformation and the repetitive structure of the original virus particle, but lack infectious genomic material. In this study, we report the production of synthetically stabilized PV VLPs in plants. Mice carrying the gene for the human PV receptor are protected from wild-type PV when immunized with the plant-made PV sVLPs. Structural analysis of the stabilized mutant at 3.6 Å resolution by cryo-electron microscopy and single-particle reconstruction reveals a structure almost indistinguishable from wild-type PV3.Despite the success of current vaccination against poliomyelitis, safe, cheap and effective vaccines remain sought for continuing eradication effort. Here the authors use plants to express stabilized virus-like particles of type 3 poliovirus that can induce a protective immune response in mice transgenic for the human poliovirus receptor. | |||||||||
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_3749.map.gz | 480.8 MB | EMDB map data format | |
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Header (meta data) | emd-3749-v30.xml emd-3749.xml | 20.5 KB 20.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3749_fsc.xml | 17.5 KB | Display | FSC data file |
Images | emd_3749.png | 326.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3749 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3749 | HTTPS FTP |
-Related structure data
Related structure data | 5o5pMC 3747C 5o5bC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3749.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | MRC format map file. Contour level determined by visual inspection in UCSF Chimera. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 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 : Human poliovirus 3
Entire | Name: Human poliovirus 3 |
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Components |
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-Supramolecule #1: Human poliovirus 3
Supramolecule | Name: Human poliovirus 3 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 Details: Poliovirus type 3 (Saukett strain) virus-like particle produced in plant expression system. NCBI-ID: 12086 / Sci species name: Human poliovirus 3 / Sci species strain: Saukett / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: Human poliovirus 3 / Strain: Saukett |
Host system | Organism: Nicotiana benthamiana (plant) / Recombinant plasmid: pEAQ-HT |
Molecular weight | Theoretical: 5.8 MDa |
Virus shell | Shell ID: 1 / Name: Capsid / Diameter: 327.0 Å / T number (triangulation number): 1 |
-Macromolecule #1: Capsid proteins, VP1
Macromolecule | Name: Capsid proteins, VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human poliovirus 3 / Strain: Saukett |
Molecular weight | Theoretical: 33.562785 KDa |
Recombinant expression | Organism: Nicotiana benthamiana (plant) |
Sequence | String: GIEDLITEVA QGALTLSLPK QQDSLPDTKA SGPAHSKEVP ALTAVETGAT NPLVPSDTVQ TRHVIQRRSR SESTIESFFA RGACVAIIE VDNEEPTTRA QKLFAMWRIT YKDTVQLRRK LEFFTYSRFD MELTFVVTAN FTNTNNGHAL NQVYQIMYIP P GAPTPKSW ...String: GIEDLITEVA QGALTLSLPK QQDSLPDTKA SGPAHSKEVP ALTAVETGAT NPLVPSDTVQ TRHVIQRRSR SESTIESFFA RGACVAIIE VDNEEPTTRA QKLFAMWRIT YKDTVQLRRK LEFFTYSRFD MELTFVVTAN FTNTNNGHAL NQVYQIMYIP P GAPTPKSW DDYTWQTSSN PSIFYTYGAA PARISVPYVG LANAYSHFYD GFAKVPLKTD ANDQIGDSLY SAMTVDDFGV LA IRVVNDH NPTKVTSKVR IYMKPKHVRV WCPRPPRAVP YYGPGVDYKD NLNPLSEKGL TTY |
-Macromolecule #2: Capsid proteins, VP2
Macromolecule | Name: Capsid proteins, VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human poliovirus 3 / Strain: Saukett |
Molecular weight | Theoretical: 30.188982 KDa |
Recombinant expression | Organism: Nicotiana benthamiana (plant) |
Sequence | String: SPNVEACGYS DRVLQLTIGN STITTQEAAN SVVAYGRWPE FIRDDEANPV DQPTEPDVAT CRFYTLDTVM WGKESKGWWW KLPDALRDM GLFGQNMYYH YLGRSGYTVH VQCNASKFHQ GALGVFAIPE YCLAGDSDKQ RYTSYANANP GEKGGKFYSQ F NRDTAVTS ...String: SPNVEACGYS DRVLQLTIGN STITTQEAAN SVVAYGRWPE FIRDDEANPV DQPTEPDVAT CRFYTLDTVM WGKESKGWWW KLPDALRDM GLFGQNMYYH YLGRSGYTVH VQCNASKFHQ GALGVFAIPE YCLAGDSDKQ RYTSYANANP GEKGGKFYSQ F NRDTAVTS PKREFCPVDY LLGCGVLLGN AFVYPHQIIN LRTNNSATIV LPYVNAMAID SMVKHNNWGI AILPLSPLDF AQ ESSVEIP ITVTIAPMCS EFNGLRNVTA PKFQ |
-Macromolecule #3: Capsid proteins, VP3
Macromolecule | Name: Capsid proteins, VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human poliovirus 3 / Strain: Saukett |
Molecular weight | Theoretical: 26.3151 KDa |
Recombinant expression | Organism: Nicotiana benthamiana (plant) |
Sequence | String: GLPVLNTPGS NQYLTSDNYQ SPCAIPEFDV TPPIDIPGEV KNMMELAEID TMIPLNLENT KRNTMDMYRV TLSDSADLSQ PILCFSLSP ASDPRLSHTM LGEVLNYYTH WAGSLKFTFL FCGSMMATGK ILVAYAPPGA QPPTSRKEAM LGTHVIWDLG L QSSCTMVV ...String: GLPVLNTPGS NQYLTSDNYQ SPCAIPEFDV TPPIDIPGEV KNMMELAEID TMIPLNLENT KRNTMDMYRV TLSDSADLSQ PILCFSLSP ASDPRLSHTM LGEVLNYYTH WAGSLKFTFL FCGSMMATGK ILVAYAPPGA QPPTSRKEAM LGTHVIWDLG L QSSCTMVV PWISNVTYRQ TTQDSFTEGG YISMFYQTRI VVPLSTPKSM SMLGFVSACN DFSVRLLRDT THISQSALPQ |
-Macromolecule #4: Capsid proteins, VP4
Macromolecule | Name: Capsid proteins, VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human poliovirus 3 / Strain: Saukett |
Molecular weight | Theoretical: 7.452113 KDa |
Recombinant expression | Organism: Nicotiana benthamiana (plant) |
Sequence | String: MGAQVSSQKV GAHENSNRAY GGSTINYTTI NYYKDSASNA ASKQDYSQDP SKFTEPLKDV LIKTAPALN |
-Macromolecule #5: 1-[5-[4-(ethoxyiminomethyl)phenoxy]-3-methyl-pentyl]-3-pyridin-4-...
Macromolecule | Name: 1-[5-[4-(ethoxyiminomethyl)phenoxy]-3-methyl-pentyl]-3-pyridin-4-yl-imidazol-2-one type: ligand / ID: 5 / Number of copies: 1 / Formula: 9LW |
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Molecular weight | Theoretical: 408.493 Da |
Chemical component information | ChemComp-9LW: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 7 / Details: PBS pH 7.0 |
Grid | Model: C-flat CF-2/1-2C / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK I / Details: Blot for 4 seconds before plunging.. |
Details | Virus-like particles for polio type 3 (strain Saukett) in complex with pocket factor compound GPP3 were assessed by negative stain EM analysis, prior to cryo-em data collection. |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 37037 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm |
Specialist optics | Energy filter - Name: GIF Quantum / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV |
Sample stage | Specimen holder model: GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
Details | Preliminary grid screening was performed. |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4086 pixel / Digitization - Dimensions - Height: 4086 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 2-25 / Number grids imaged: 1 / Number real images: 1018 / Average exposure time: 0.2 sec. / Average electron dose: 1.2 e/Å2 |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Details | phenix.real_space_refine was used to refine the atomic model in the cryo-em map. |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient |
Output model | PDB-5o5p: |