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Yorodumi- EMDB-1058: The structure of echovirus type 12 bound to a two-domain fragment... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1058 | |||||||||
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Title | The structure of echovirus type 12 bound to a two-domain fragment of its cellular attachment protein decay-accelerating factor (CD 55). | |||||||||
Map data | Reconstruction of Echovirus type 12 from cryo-negative stain image data | |||||||||
Sample |
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Function / homology | Function and homology information negative regulation of complement activation / regulation of lipopolysaccharide-mediated signaling pathway / regulation of complement-dependent cytotoxicity / regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ficolin-1-rich granule membrane ...negative regulation of complement activation / regulation of lipopolysaccharide-mediated signaling pathway / regulation of complement-dependent cytotoxicity / regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ficolin-1-rich granule membrane / side of membrane / COPI-mediated anterograde transport / complement activation, classical pathway / transport vesicle / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / endoplasmic reticulum-Golgi intermediate compartment membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / secretory granule membrane / host cell cytoplasmic vesicle membrane / Regulation of Complement cascade / endocytosis involved in viral entry into host cell / cytoplasmic vesicle membrane / positive regulation of T cell cytokine production / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / virus receptor activity / monoatomic ion channel activity / positive regulation of cytosolic calcium ion concentration / RNA helicase activity / DNA replication / induction by virus of host autophagy / RNA-directed RNA polymerase / membrane raft / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / Golgi membrane / innate immune response / DNA-templated transcription / lipid binding / Neutrophil degranulation / structural molecule activity / virion attachment to host cell / cell surface / ATP hydrolysis activity / proteolysis / RNA binding / extracellular exosome / extracellular region / ATP binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Human echovirus 12 | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 18.0 Å | |||||||||
Authors | Bhella D / Goodfellow IG / Roversi P / Pettigrew D / Chaudhry Y / Evans DJ / Lea SM | |||||||||
Citation | Journal: J Biol Chem / Year: 2004 Title: The structure of echovirus type 12 bound to a two-domain fragment of its cellular attachment protein decay-accelerating factor (CD 55). Authors: David Bhella / Ian G Goodfellow / Pietro Roversi / David Pettigrew / Yasmin Chaudhry / David J Evans / Susan M Lea / Abstract: Echovirus type 12 (EV12), an Enterovirus of the Picornaviridae family, uses the complement regulator decay-accelerating factor (DAF, CD55) as a cellular receptor. We have calculated a three- ...Echovirus type 12 (EV12), an Enterovirus of the Picornaviridae family, uses the complement regulator decay-accelerating factor (DAF, CD55) as a cellular receptor. We have calculated a three-dimensional reconstruction of EV12 bound to a fragment of DAF consisting of short consensus repeat domains 3 and 4 from cryo-negative stain electron microscopy data (EMD code 1057). This shows that, as for an earlier reconstruction of the related echovirus type 7 bound to DAF, attachment is not within the viral canyon but occurs close to the 2-fold symmetry axes. Despite this general similarity our reconstruction reveals a receptor interaction that is quite different from that observed for EV7. Fitting of the crystallographic co-ordinates for DAF(34) and EV11 into the reconstruction shows a close agreement between the crystal structure of the receptor fragment and the density for the virus-bound receptor, allowing unambiguous positioning of the receptor with respect to the virion (PDB code 1UPN). Our finding that the mode of virus-receptor interaction in EV12 is distinct from that seen for EV7 raises interesting questions regarding the evolution and biological significance of the DAF binding phenotype in these viruses. | |||||||||
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_1058.map.gz | 987.8 KB | EMDB map data format | |
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Header (meta data) | emd-1058-v30.xml emd-1058.xml | 9.7 KB 9.7 KB | Display Display | EMDB header |
Images | 1058.gif | 71.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1058 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1058 | HTTPS FTP |
-Related structure data
Related structure data | 1upnMC 1057C 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_1058.map.gz / Format: CCP4 / Size: 20 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of Echovirus type 12 from cryo-negative stain image data | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.42 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 : Echovirus type 12
Entire | Name: Echovirus type 12 |
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Components |
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-Supramolecule #1000: Echovirus type 12
Supramolecule | Name: Echovirus type 12 / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: Human echovirus 12
Supramolecule | Name: Human echovirus 12 / type: virus / ID: 1 / Name.synonym: EV12 / NCBI-ID: 35293 / Sci species name: Human echovirus 12 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No / Syn species name: EV12 |
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Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.4 / Details: PBS A |
Staining | Type: NEGATIVE Details: Absorb protein to grid, float on 20% ammonium molybdate pH 7.4 for 10 seconds blot and plunge |
Grid | Details: 400 mesh Quantifoils |
Vitrification | Cryogen name: ETHANE / Method: blot for 2 seconds, wait for 2 seconds, plunge |
-Electron microscopy
Microscope | JEOL 1200EXII |
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Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Calibrated magnification: 29200 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 3.4 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 30000 |
Sample stage | Specimen holder: side entry / Specimen holder model: OTHER |
Alignment procedure | Legacy - Astigmatism: objective lens corrected at 200k x |
Details | MICROSCOPE JEOL 1200 EX with OXFORD INSTRUMENTS CRYO-TRANSFER STAGE |
Image recording | Category: CCD / Film or detector model: KODAK SO-163 FILM / Digitization - Sampling interval: 3.42 µm / Number real images: 28 / Details: Scanned with a Dunvegan HiScan / Bits/pixel: 16 |
-Image processing
CTF correction | Details: merge of focal pair images of single particles |
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Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EM3DR2, PFT2, CTFMIX Details: Particles were aligned using a model based strategy starting with a model derived from the crystallographic co-ordinates of EV-1, filtered to 16 Angstroms resolution. The program is called ...Details: Particles were aligned using a model based strategy starting with a model derived from the crystallographic co-ordinates of EV-1, filtered to 16 Angstroms resolution. The program is called PFT (Polar Fourier Transform). The reconstructions were calculated using the EM3DR2 program which is based on the standard method of calculating icosahedral reconstructions as described by Crowther,'Fourier-Bessel'. Number images used: 617 |
-Atomic model buiding 1
Details | 3D crystal structure fitting details lodged with PDB 1UPN |
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Output model | PDB-1upn: |