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- PDB-4q4y: Crystal structure of Coxsackievirus A24v soaked with Disialyllact... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4q4y | ||||||
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Title | Crystal structure of Coxsackievirus A24v soaked with Disialyllacto-N-tetraose (DSLNT) | ||||||
![]() | (Coxsackievirus capsid protein ...) x 4 | ||||||
![]() | VIRUS / Coxsackievirus A24v | ||||||
Function / homology | ![]() 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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase ...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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / symbiont-mediated suppression of host innate immune response / 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 / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zocher, G. / Stehle, T. | ||||||
![]() | ![]() Title: A sialic Acid binding site in a human picornavirus. Authors: Zocher, G. / Mistry, N. / Frank, M. / Hahnlein-Schick, I. / Ekstrom, J.O. / Arnberg, N. / Stehle, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 196.5 KB | Display | ![]() |
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PDB format | ![]() | 156.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Components
-Coxsackievirus capsid protein ... , 4 types, 4 molecules 1234
#1: Protein | Mass: 34378.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 29817.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: Protein | Mass: 26637.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#4: Protein | Mass: 7319.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Sugars , 1 types, 1 molecules ![](data/chem/img/SIA.gif)
#5: Sugar | ChemComp-SIA / |
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-Non-polymers , 6 types, 809 molecules ![](data/chem/img/HEZ.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MYR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MYR.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | #7: Chemical | ChemComp-CA / #8: Chemical | ChemComp-CL / #9: Chemical | ChemComp-MG / | #10: Chemical | ChemComp-MYR / | #11: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 200 mM Magnesium chloride, 3.4 M 1,6-Hexanediol, 100 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 20, 2012 |
Radiation | Monochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→49.78 Å / Num. all: 1626655 / Num. obs: 1552490 / % possible obs: 95.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.39 Å2
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Refinement step | Cycle: LAST / Resolution: 1.88→49.78 Å
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Refine LS restraints |
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