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Yorodumi- PDB-4q4y: Crystal structure of Coxsackievirus A24v soaked with Disialyllact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q4y | ||||||
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Title | Crystal structure of Coxsackievirus A24v soaked with Disialyllacto-N-tetraose (DSLNT) | ||||||
Components | (Coxsackievirus capsid protein ...) x 4 | ||||||
Keywords | VIRUS / Coxsackievirus A24v | ||||||
Function / homology | Function and homology information 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 / 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 / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Coxsackievirus A24 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | ||||||
Authors | Zocher, G. / Stehle, T. | ||||||
Citation | Journal: Plos Pathog. / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q4y.cif.gz | 196.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q4y.ent.gz | 156.4 KB | Display | PDB format |
PDBx/mmJSON format | 4q4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4q4y_validation.pdf.gz | 813.2 KB | Display | wwPDB validaton report |
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Full document | 4q4y_full_validation.pdf.gz | 815.6 KB | Display | |
Data in XML | 4q4y_validation.xml.gz | 39.1 KB | Display | |
Data in CIF | 4q4y_validation.cif.gz | 59 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/4q4y ftp://data.pdbj.org/pub/pdb/validation_reports/q4/4q4y | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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6 |
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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) Coxsackievirus A24 / References: UniProt: V9VEF3 |
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#2: Protein | Mass: 29817.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A24 / References: UniProt: V9VEF3 |
#3: Protein | Mass: 26637.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A24 / References: UniProt: V9VEF3 |
#4: Protein | Mass: 7319.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A24 / References: UniProt: V9VEF3 |
-Sugars , 1 types, 1 molecules
#5: Sugar | ChemComp-SIA / |
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-Non-polymers , 6 types, 809 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→49.78 Å / Cor.coef. Fo:Fc: 0.958 / SU B: 2.084 / SU ML: 0.058 / ESU R: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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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