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Yorodumi- EMDB-15725: Poliovirus type 3 (strain Saukett) stabilised virus-like particle... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15725 | |||||||||
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Title | Poliovirus type 3 (strain Saukett) stabilised virus-like particle (PV3 SC8) in complex with GSH and GPP3 | |||||||||
Map data | Local resolution scaled final map from RELION. Contour level determined in UCSF ChimeraX | |||||||||
Sample |
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Keywords | Capsid protein / VIRUS LIKE PARTICLE / Glutathione / inhibitor / complex | |||||||||
Function / homology | Function and homology information symbiont genome entry into host cell via pore formation in plasma membrane / symbiont-mediated suppression of host gene expression / viral capsid / virion attachment to host cell / structural molecule activity Similarity search - Function | |||||||||
Biological species | Human poliovirus 3 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.5 Å | |||||||||
Authors | Bahar MW / Fry EE / Stuart DI | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Commun Biol / Year: 2022 Title: A conserved glutathione binding site in poliovirus is a target for antivirals and vaccine stabilisation. Authors: Mohammad W Bahar / Veronica Nasta / Helen Fox / Lee Sherry / Keith Grehan / Claudine Porta / Andrew J Macadam / Nicola J Stonehouse / David J Rowlands / Elizabeth E Fry / David I Stuart / Abstract: Strategies to prevent the recurrence of poliovirus (PV) after eradication may utilise non-infectious, recombinant virus-like particle (VLP) vaccines. Despite clear advantages over inactivated or ...Strategies to prevent the recurrence of poliovirus (PV) after eradication may utilise non-infectious, recombinant virus-like particle (VLP) vaccines. Despite clear advantages over inactivated or attenuated virus vaccines, instability of VLPs can compromise their immunogenicity. Glutathione (GSH), an important cellular reducing agent, is a crucial co-factor for the morphogenesis of enteroviruses, including PV. We report cryo-EM structures of GSH bound to PV serotype 3 VLPs showing that it can enhance particle stability. GSH binds the positively charged pocket at the interprotomer interface shown recently to bind GSH in enterovirus F3 and putative antiviral benzene sulphonamide compounds in other enteroviruses. We show, using high-resolution cryo-EM, the binding of a benzene sulphonamide compound with a PV serotype 2 VLP, consistent with antiviral activity through over-stabilizing the interprotomer pocket, preventing the capsid rearrangements necessary for viral infection. Collectively, these results suggest GSH or an analogous tight-binding antiviral offers the potential for stabilizing VLP vaccines. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15725.map.gz | 193.7 MB | EMDB map data format | |
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Header (meta data) | emd-15725-v30.xml emd-15725.xml | 24.7 KB 24.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15725_fsc.xml | 15.8 KB | Display | FSC data file |
Images | emd_15725.png | 93 KB | ||
Filedesc metadata | emd-15725.cif.gz | 7.8 KB | ||
Others | emd_15725_half_map_1.map.gz emd_15725_half_map_2.map.gz | 275.2 MB 275.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15725 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15725 | HTTPS FTP |
-Related structure data
Related structure data | 8ayxMC 8ayyC 8ayzC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_15725.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Local resolution scaled final map from RELION. Contour level determined in UCSF ChimeraX | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map from final refinement in RELION. Contour...
File | emd_15725_half_map_1.map | ||||||||||||
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Annotation | Half map from final refinement in RELION. Contour level determined in UCSF ChimeraX. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map from final refinement in RELION. Contour...
File | emd_15725_half_map_2.map | ||||||||||||
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Annotation | Half map from final refinement in RELION. Contour level determined in UCSF ChimeraX. | ||||||||||||
Projections & Slices |
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Density Histograms |
-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-#3 Details: Recombinantly expressed virus-like particle of poliovirus type 3 (strain Saukett). 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: Homo sapiens (human) |
Molecular weight | Theoretical: 5.85 MDa |
Virus shell | Shell ID: 1 / Name: Virus shell 1 / Diameter: 310.0 Å / T number (triangulation number): 1 |
-Macromolecule #1: Capsid protein, VP1
Macromolecule | Name: Capsid protein, 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: Komagataella pastoris (fungus) |
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 UniProtKB: Genome polyprotein |
-Macromolecule #2: Capsid protein, VP0
Macromolecule | Name: Capsid protein, VP0 / type: protein_or_peptide / ID: 2 Details: Sequence is given for the VP0 polypeptide. Mutations are numbered according to sequence numbering for mature polypeptides VP2 and VP4. Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human poliovirus 3 / Strain: Saukett |
Molecular weight | Theoretical: 37.623023 KDa |
Recombinant expression | Organism: Komagataella pastoris (fungus) |
Sequence | String: MGAQVSSQKV GAHENSNRAY GGSTINYTTI NYYKDSASNA ASKQDYSQDP SKFTEPLKDV LIKTAPALNS PNVEACGYSD RVLQLTIGN STITTQEAAN SVVAYGRWPE FIRDDEANPV DQPTEPDVAT CRFYTLDTVM WGKESKGWWW KLPDALRDMG L FGQNMYYH ...String: MGAQVSSQKV GAHENSNRAY GGSTINYTTI NYYKDSASNA ASKQDYSQDP SKFTEPLKDV LIKTAPALNS PNVEACGYSD RVLQLTIGN STITTQEAAN SVVAYGRWPE FIRDDEANPV DQPTEPDVAT CRFYTLDTVM WGKESKGWWW KLPDALRDMG L FGQNMYYH YLGRSGYTVH VQCNASKFHQ GALGVFAIPE YCLAGDSDKQ RYTSYANANP GEKGGKFYSQ FNRDTAVTSP KR EFCPVDY LLGCGVLLGN AFVYPHQIIN LRTNNSATIV LPYVNAMAID SMVKHNNWGI AILPLSPLDF AQESSVEIPI TVT IAPMCS EFNGLRNVTA PKFQ UniProtKB: Genome polyprotein |
-Macromolecule #3: Capsid protein, VP3
Macromolecule | Name: Capsid protein, 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: Komagataella pastoris (fungus) |
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 UniProtKB: Genome polyprotein |
-Macromolecule #4: 1-[(3S)-5-[4-[(E)-ETHOXYIMINOMETHYL]PHENOXY]-3-METHYL-PENTYL]-3-P...
Macromolecule | Name: 1-[(3S)-5-[4-[(E)-ETHOXYIMINOMETHYL]PHENOXY]-3-METHYL-PENTYL]-3-PYRIDIN-4-YL-IMIDAZOLIDIN-2-ONE type: ligand / ID: 4 / Number of copies: 1 / Formula: YM2 |
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Molecular weight | Theoretical: 410.509 Da |
Chemical component information | ChemComp-YM2: |
-Macromolecule #5: GLUTATHIONE
Macromolecule | Name: GLUTATHIONE / type: ligand / ID: 5 / Number of copies: 1 / Formula: GSH |
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Molecular weight | Theoretical: 307.323 Da |
Chemical component information | ChemComp-GSH: |
-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 / Component:
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Grid | Model: EMS Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Support film - Film thickness: 3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR Details: The specific type of grid used was Ultra-thin carbon support film, 3nm - on lacey carbon AGS187-4 from Agar Scientific. | ||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV Details: 4 ul of sample blotted for 3.5 seconds with -15 blot force on FEI Vitrobot mark IV.. | ||||||
Details | Virus-like particle purified by sucrose density gradient purification from Pichia pastoris cells. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2503 / Average exposure time: 69.78 sec. / Average electron dose: 34.89 e/Å2 / Details: Pixel sampling of 1.08 A/pixel. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated magnification: 129629 / Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal defocus max: 2.9 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Details | Initial model was rigid body fitted using UCSF chimera and Coot. Global minimization and B-factor refinement was performed in real space using phenix_real.space.refine. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient |
Output model | PDB-8ayx: |