|Entry||Database: EMDB / ID: EMD-5286|
|Title||Poliovirus 80S particle and P1 Fab complex with Fab bound at propeller tip|
|Sample||Poliovirus 80S particle and P1(monospecific antibody) Fab complex:|
|Keywords||picornavirus / viral cell entry / viral uncoating / virus-antibody complex / virus-Fab complex / virus disassembly / virus uncoating / virus conformational transitions / monospecific antibody|
|Biological species||Human poliovirus 1 Mahoney (poliovirus 80S)|
|Method||single particle reconstruction / cryo EM / Resolution: 18 Å|
|Authors||Lin J / Cheng N / Chow M / Filman DJ / Steven AC / Hogle JM / Belnap DM|
|Citation||Journal: J. Virol. / Year: 2011|
Title: An externalized polypeptide partitions between two distinct sites on genome-released poliovirus particles.
Authors: Jun Lin / Naiqian Cheng / Marie Chow / David J Filman / Alasdair C Steven / James M Hogle / David M Belnap /
Abstract: During cell entry, native poliovirus (160S) converts to a cell-entry intermediate (135S) particle, resulting in the externalization of capsid proteins VP4 and the amino terminus of VP1 (residues 1 to ...During cell entry, native poliovirus (160S) converts to a cell-entry intermediate (135S) particle, resulting in the externalization of capsid proteins VP4 and the amino terminus of VP1 (residues 1 to 53). Externalization of these entities is followed by release of the RNA genome (uncoating), leaving an empty (80S) particle. The antigen-binding fragment (Fab) of a monospecific peptide 1 (P1) antibody, which was raised against a peptide corresponding to amino-terminal residues 24 to 40 of VP1, was utilized to track the location of the amino terminus of VP1 in the 135S and 80S states of poliovirus particles via cryogenic electron microscopy (cryo-EM) and three-dimensional image reconstruction. On 135S, P1 Fabs bind to a prominent feature on the external surface known as the "propeller tip." In contrast, our initial 80S-P1 reconstruction showed P1 Fabs also binding to a second site, at least 50 Å distant, at the icosahedral 2-fold axes. Further analysis showed that the overall population of 80S-P1 particles consisted of three kinds of capsids: those with P1 Fabs bound only at the propeller tips, P1 Fabs bound only at the 2-fold axes, or P1 Fabs simultaneously bound at both positions. Our results indicate that, in 80S particles, a significant fraction of VP1 can deviate from icosahedral symmetry. Hence, this portion of VP1 does not change conformation synchronously when switching from the 135S state. These conclusions are compatible with previous observations of multiple conformations of the 80S state and suggest that movement of the amino terminus of VP1 has a role in uncoating. Similar deviations from icosahedral symmetry may be biologically significant during other viral transitions.
|Structure viewer||EM map: |
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|File||Download / File: emd_5286.map.gz / Format: CCP4 / Size: 70.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.83 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Poliovirus 80S particle and P1(monospecific antibody) Fab complex
|Entire||Name: Poliovirus 80S particle and P1(monospecific antibody) Fab complex|
Number of components: 2 / Oligomeric State: 80S particle icosahedral with Fab
-Component #1: virus, Human poliovirus 1 Mahoney
|Virus||Name: Human poliovirus 1 Mahoney / a.k.a: poliovirus 80S / Class: VIRION|
Details: native virus 160S is converted by heat-treatment to 80S
Empty: Yes / Enveloped: No / Isolate: STRAIN
|Species||Species: Human poliovirus 1 Mahoney (poliovirus 80S)|
|Source (natural)||Host Species: Homo sapiens (human) / Host category: VERTEBRATES|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||Buffer solution: 20 mM Tris, 2 mM CaCl2 / pH: 7.5|
|Vitrification||Cryogen name: ETHANE / Method: Blotted manually before plunging|
Details: Vitrification carried out in ambient atmosphere. Ethane cooled by liquid nitrogen.
-Electron microscopy imaging
|Imaging||Microscope: FEI/PHILIPS CM200FEG / Date: Jul 15, 1999|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 10 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 38000 X (nominal), 37752 X (calibrated) / Astigmatism: Bsoft / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 810 - 2240 nm|
|Specimen Holder||Holder: Side entry liquid nitrogen-cooled cryo specimen holder|
Model: GATAN LIQUID NITROGEN
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 14 / Scanner: ZEISS SCAI / Sampling size: 7 µm / Bit depth: 8 / Details: Defocal pairs were used.|
|Processing||Method: single particle reconstruction / Number of projections: 1132 / Applied symmetry: I (icosahedral)|
|3D reconstruction||Algorithm: Fourier Bessel / Software: EM3DR2 / CTF correction: CTF and decay correction of each particle|
Details: Reconstruction computed from focal pairs. Pairs not summed for reconstruction calculation.
Resolution: 18 Å / Resolution method: FSC 0.5
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