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- EMDB-5888: Electron cryo-microscopy of nanobody AB29 in complex with poliovi... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-5888 | |||||||||
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Title | Electron cryo-microscopy of nanobody AB29 in complex with poliovirus P1/Mahoney | |||||||||
![]() | reconstruction of nanobody AB29 in complex with poliovirus P1/Mahoney | |||||||||
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Function / homology | ![]() symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Schotte L / Strauss M / Thys B / Halewyck H / Filman DJ / Bostina M / Hogle JM / Rombaut B | |||||||||
![]() | ![]() Title: Five of Five VHHs Neutralizing Poliovirus Bind the Receptor-Binding Site. Authors: Mike Strauss / Lise Schotte / Bert Thys / David J Filman / James M Hogle / ![]() ![]() Abstract: Nanobodies, or VHHs, that recognize poliovirus type 1 have previously been selected and characterized as candidates for antiviral agents or reagents for standardization of vaccine quality control. In ...Nanobodies, or VHHs, that recognize poliovirus type 1 have previously been selected and characterized as candidates for antiviral agents or reagents for standardization of vaccine quality control. In this study, we present high-resolution cryo-electron microscopy reconstructions of poliovirus with five neutralizing VHHs. All VHHs bind the capsid in the canyon at sites that extensively overlap the poliovirus receptor-binding site. In contrast, the interaction involves a unique (and surprisingly extensive) surface for each of the five VHHs. Five regions of the capsid were found to participate in binding with all five VHHs. Four of these five regions are known to alter during the expansion of the capsid associated with viral entry. Interestingly, binding of one of the VHHs, PVSS21E, resulted in significant changes of the capsid structure and thus seems to trap the virus in an early stage of expansion. IMPORTANCE: We describe the cryo-electron microscopy structures of complexes of five neutralizing VHHs with the Mahoney strain of type 1 poliovirus at resolutions ranging from 3.8 to 6.3Å. All five ...IMPORTANCE: We describe the cryo-electron microscopy structures of complexes of five neutralizing VHHs with the Mahoney strain of type 1 poliovirus at resolutions ranging from 3.8 to 6.3Å. All five VHHs bind deep in the virus canyon at similar sites that overlap extensively with the binding site for the receptor (CD155). The binding surfaces on the VHHs are surprisingly extensive, but despite the use of similar binding surfaces on the virus, the binding surface on the VHHs is unique for each VHH. In four of the five complexes, the virus remains essentially unchanged, but for the fifth there are significant changes reminiscent of but smaller in magnitude than the changes associated with cell entry, suggesting that this VHH traps the virus in a previously undescribed early intermediate state. The neutralizing mechanisms of the VHHs and their potential use as quality control agents for the end game of poliovirus eradication are discussed. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 111.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.5 KB 14.5 KB | Display Display | ![]() |
Images | ![]() | 393.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3jbcM ![]() 5886C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | reconstruction of nanobody AB29 in complex with poliovirus P1/Mahoney | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.681 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : nanobody AB29 in complex with poliovirus P1/Mahoney
Entire | Name: nanobody AB29 in complex with poliovirus P1/Mahoney |
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Components |
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-Supramolecule #1000: nanobody AB29 in complex with poliovirus P1/Mahoney
Supramolecule | Name: nanobody AB29 in complex with poliovirus P1/Mahoney / type: sample / ID: 1000 / Details: 1 Oligomeric state: 60 nanobody VHH monomers bind to each poliovirion Number unique components: 2 |
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Molecular weight | Experimental: 9.0 MDa / Theoretical: 9.0 MDa / Method: 1 |
-Supramolecule #1: Human poliovirus 1
Supramolecule | Name: Human poliovirus 1 / type: virus / ID: 1 / NCBI-ID: 12080 / Sci species name: Human poliovirus 1 / Database: NCBI / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No / Sci species serotype: Mahoney |
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Host (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 9 MDa / Theoretical: 9 MDa |
Virus shell | Shell ID: 1 / Diameter: 350 Å / T number (triangulation number): 1 |
-Macromolecule #1: nanobody PVSP29F
Macromolecule | Name: nanobody PVSP29F / type: protein_or_peptide / ID: 1 / Name.synonym: nanobody AB29 Details: Each virus is decorated with 60 copies of nanobody PVSP29F. Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() ![]() |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.4 / Details: 145 mM NaCl, 50 mM Na2HPO4.12H2O |
Grid | Details: Quantifoil R2/2 |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 154 K / Instrument: HOMEMADE PLUNGER |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 89232 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Date | Oct 23, 2012 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 1503 / Average electron dose: 25 e/Å2 / Bits/pixel: 16 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
CTF correction | Details: per particle |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: OTHER / Software - Name: Frealign / Number images used: 9764 |
Details | The particles were processed using Frealign. |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: REFMAC5, COOT, SPDBV |
Details | Rigid body with some flexible loops and side chains. LSQKAB was applied after each refinement cycle to re-impose exact icosahedral operators and rigid body constraints. |
Refinement | Space: RECIPROCAL / Protocol: RIGID BODY FIT Target criteria: Stereochemically restrained maximum likelihood refinement of both Fourier phase and amplitude agreement |
Output model | ![]() PDB-3jbc: |
-Atomic model buiding 2
Initial model | PDB ID: |
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Software | Name: REFMAC5, COOT, SPDBV |
Details | Rigid body with some flexible loops and side chains. LSQKAB was applied after each refinement cycle to re-impose exact icosahedral operators and rigid body constraints. |
Refinement | Space: RECIPROCAL / Protocol: RIGID BODY FIT Target criteria: Stereochemically restrained maximum likelihood refinement of both Fourier phase and amplitude agreement |
Output model | ![]() PDB-3jbc: |
-Atomic model buiding 3
Initial model | PDB ID: |
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Software | Name: REFMAC5, COOT, SPDBV |
Details | Rigid body with some flexible loops and side chains. LSQKAB was applied after each refinement cycle to re-impose exact icosahedral operators and rigid body constraints. |
Refinement | Space: RECIPROCAL / Protocol: RIGID BODY FIT Target criteria: Stereochemically restrained maximum likelihood refinement of both Fourier phase and amplitude agreement |
Output model | ![]() PDB-3jbc: |