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Yorodumi- EMDB-5291: Poliovirus 160S particle and C3 Fab complex at 11.1 Angstrom reso... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5291 | |||||||||
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Title | Poliovirus 160S particle and C3 Fab complex at 11.1 Angstrom resolution | |||||||||
Map data | This is a map of poliovirus 160S particle and C3 Fab complex. | |||||||||
Sample |
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Keywords | poliovirus / antibody-antigen interactions / antibody-protein interactions / C3 antibody / fragment antibody-binding (Fab) / picornavirus / virus-antibody interactions | |||||||||
Function / homology | Function and homology information 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 / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid ...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 / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / channel activity / nucleoside-triphosphate phosphatase / monoatomic ion transmembrane transport / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) / Human poliovirus 1 Mahoney | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 11.1 Å | |||||||||
Authors | Lin J / Cheng N / Hogle JM / Steven AC / Belnap DM | |||||||||
Citation | Journal: J Immunol / Year: 2013 Title: Conformational shift of a major poliovirus antigen confirmed by immuno-cryogenic electron microscopy. Authors: Jun Lin / Naiqian Cheng / James M Hogle / Alasdair C Steven / David M Belnap / Abstract: Small, interfacial conformational changes occur in some Ag-Ab interactions. Using cryogenic electron microscopy (cryo-EM), we have demonstrated such changes in a major antigenic site of a poliovirus ...Small, interfacial conformational changes occur in some Ag-Ab interactions. Using cryogenic electron microscopy (cryo-EM), we have demonstrated such changes in a major antigenic site of a poliovirus capsid protein. During cell entry, native human poliovirus (160S particle) converts to a cell entry intermediate (135S particle) and later to an RNA-released (80S) particle. By mixing particles with Fabs of the neutralizing C3 mAb, we labeled the external loop connecting the B and C β-strands (BC loop) of the capsid protein VP1 (residues 95-105) in the 160S and 135S states. We then determined three-dimensional structures by cryo-EM and enhanced their interpretability by fitting high-resolution coordinates of C3 Fab and the capsid proteins into the density maps. Binding of C3 to either 160S or 135S particles caused residues of the BC loop, located on the tip of a prominent peak known as the "mesa," to move by an estimated 5 Å. C3 Abs are neutralizing and can bind bivalently. The orientation of the bound Fabs in our reconstructions suggests that C3 neutralizes poliovirus by binding two adjacent BC loops on the same mesa and inhibiting conformational changes in the viral capsid. | |||||||||
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_5291.map.gz | 27.2 MB | EMDB map data format | |
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Header (meta data) | emd-5291-v30.xml emd-5291.xml | 11.6 KB 11.6 KB | Display Display | EMDB header |
Images | emd_5291_1.jpg | 73.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5291 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5291 | HTTPS FTP |
-Validation report
Summary document | emd_5291_validation.pdf.gz | 326.8 KB | Display | EMDB validaton report |
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Full document | emd_5291_full_validation.pdf.gz | 326.4 KB | Display | |
Data in XML | emd_5291_validation.xml.gz | 6.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5291 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5291 | HTTPS FTP |
-Related structure data
Related structure data | 3j3oMC 5292C 5293C 3j3pC 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_5291.map.gz / Format: CCP4 / Size: 56.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a map of poliovirus 160S particle and C3 Fab complex. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.824 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 : Poliovirus 160S particle and C3 Fab complex
Entire | Name: Poliovirus 160S particle and C3 Fab complex |
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Components |
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-Supramolecule #1000: Poliovirus 160S particle and C3 Fab complex
Supramolecule | Name: Poliovirus 160S particle and C3 Fab complex / type: sample / ID: 1000 / Oligomeric state: 160S particle icosahedral with Fab / Number unique components: 2 |
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-Supramolecule #1: Human poliovirus 1 Mahoney
Supramolecule | Name: Human poliovirus 1 Mahoney / type: virus / ID: 1 / NCBI-ID: 12081 / Sci species name: Human poliovirus 1 Mahoney / Sci species strain: Mahoney / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
Virus shell | Shell ID: 1 / Diameter: 325 Å / T number (triangulation number): 1 |
-Macromolecule #1: C3 Fab
Macromolecule | Name: C3 Fab / type: protein_or_peptide / ID: 1 / Name.synonym: C3 Fab / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 / Details: 20 mM Tris, 2 mM CaCl2 |
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Vitrification | Cryogen name: ETHANE / Instrument: OTHER Details: Vitrification carried out in ambient atmosphere. Ethane cooled by liquid nitrogen. Method: Blotted manually before plunging |
-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
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Alignment procedure | Legacy - Astigmatism: Bsoft |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 12 / Average electron dose: 10 e/Å2 / Details: Defocal pairs were used. / Bits/pixel: 8 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 37587 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 1.77 µm / Nominal defocus min: 0.73 µm / Nominal magnification: 38000 |
Sample stage | Specimen holder: Side entry liquid nitrogen-cooled cryo specimen holder Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
CTF correction | Details: CTF and decay correction of each particle |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EM3DR2 Details: Reconstruction computed from focal pairs. Pairs not summed for reconstruction calculation. Number images used: 4184 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: L / Chain - #1 - Chain ID: H / Chain - #2 - Chain ID: P |
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Software | Name: CHARMM |
Details | PDBEntryID_givenInChain. Protocol: Rigid Body. Atomic coordinates for the C3 Fab (Nature Struct. Biol. 2, 232-243) (1FPT in Protein Data Bank) were first fitted manually (by eye) via UCSF Chimera package (Journal of Computational Chemistry 25, 1605-1612). Next, a core-weighted, rigid-body fitting algorithm, implemented in CHARRM (J Struct Biol 141, 63-76), was used to refine the fit. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-3j3o: |