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Yorodumi- EMDB-5292: Poliovirus 135S particle and C3 Fab complex at 9.1 Angstrom resolution -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5292 | |||||||||
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Title | Poliovirus 135S particle and C3 Fab complex at 9.1 Angstrom resolution | |||||||||
Map data | This is a map of poliovirus 135S particle and C3 Fab complex. | |||||||||
Sample |
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Keywords | 135S cell-entry intermediate particle / 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 / positive regulation of B cell activation / humoral immune response mediated by circulating immunoglobulin / early endosome to late endosome transport / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / endosome to lysosome transport ...symbiont-mediated suppression of host translation initiation / positive regulation of B cell activation / humoral immune response mediated by circulating immunoglobulin / early endosome to late endosome transport / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / endosome to lysosome transport / phagocytosis, engulfment / positive regulation of endocytosis / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / antigen processing and presentation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / immunoglobulin mediated immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of phagocytosis / 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 / multivesicular body / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / complement activation, classical pathway / T=pseudo3 icosahedral viral capsid / antigen binding / host cell cytoplasmic vesicle membrane / response to bacterium / endocytosis involved in viral entry into host cell / positive regulation of immune response / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / antibacterial humoral response / RNA helicase activity / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Human poliovirus 1 Mahoney | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.1 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_5292.map.gz | 34.5 MB | EMDB map data format | |
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Header (meta data) | emd-5292-v30.xml emd-5292.xml | 11.2 KB 11.2 KB | Display Display | EMDB header |
Images | emd_5292_1.jpg | 77.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5292 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5292 | HTTPS FTP |
-Validation report
Summary document | emd_5292_validation.pdf.gz | 369 KB | Display | EMDB validaton report |
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Full document | emd_5292_full_validation.pdf.gz | 368.6 KB | Display | |
Data in XML | emd_5292_validation.xml.gz | 6.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5292 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5292 | HTTPS FTP |
-Related structure data
Related structure data | 3j3pMC 5291C 5293C 3j3oC 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_5292.map.gz / Format: CCP4 / Size: 70.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a map of poliovirus 135S particle and C3 Fab complex. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.84 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 135S particle and C3 Fab complex
Entire | Name: Poliovirus 135S particle and C3 Fab complex |
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Components |
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-Supramolecule #1000: Poliovirus 135S particle and C3 Fab complex
Supramolecule | Name: Poliovirus 135S particle and C3 Fab complex / type: sample / ID: 1000 / Oligomeric state: 135S 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 Details: native virus 160S is converted by heat treatment to 135S 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: 340 Å / T number (triangulation number): 1 |
-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: 4 / 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: 38000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 1.63 µm / Nominal defocus min: 1.12 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: 9.1 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: 9810 |
-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-3j3p: |