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Yorodumi- PDB-7oj7: Crystal structure of human coxsackievirus A24v in complex with a ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7oj7 | |||||||||
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Title | Crystal structure of human coxsackievirus A24v in complex with a pentavalent N-acetylneuraminic acid conjugate | |||||||||
Components | (Capsid protein ...) x 4 | |||||||||
Keywords | VIRUS / human Coxsackievirus A24v / starfish-like inhibitor / corannulene | |||||||||
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 / symbiont-mediated suppression of host gene expression / 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 / 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: 1.78 Å | |||||||||
Authors | Zocher, G. / Stehle, T. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Int J Mol Sci / Year: 2021 Title: Exploring the Effect of Structure-Based Scaffold Hopping on the Inhibition of Coxsackievirus A24v Transduction by Pentavalent N-Acetylneuraminic Acid Conjugates. Authors: Emil Johansson / Rémi Caraballo / Daniel L Hurdiss / Nitesh Mistry / C David Andersson / Rebecca F Thompson / Neil A Ranson / Georg Zocher / Thilo Stehle / Niklas Arnberg / Mikael Elofsson / Abstract: Coxsackievirus A24 variant (CVA24v) is the primary causative agent of the highly contagious eye infection designated acute hemorrhagic conjunctivitis (AHC). It is solely responsible for two pandemics ...Coxsackievirus A24 variant (CVA24v) is the primary causative agent of the highly contagious eye infection designated acute hemorrhagic conjunctivitis (AHC). It is solely responsible for two pandemics and several recurring outbreaks of the disease over the last decades, thus affecting millions of individuals throughout the world. To date, no antiviral agents or vaccines are available for combating this disease, and treatment is mainly supportive. CVA24v utilizes Neu5Ac-containing glycans as attachment receptors facilitating entry into host cells. We have previously reported that pentavalent Neu5Ac conjugates based on a glucose-scaffold inhibit CVA24v infection of human corneal epithelial cells. In this study, we report on the design and synthesis of scaffold-replaced pentavalent Neu5Ac conjugates and their effect on CVA24v cell transduction and the use of cryogenic electron microscopy (cryo-EM) to study the binding of these multivalent conjugates to CVA24v. The results presented here provide insights into the development of Neu5Ac-based inhibitors of CVA24v and, most significantly, the first application of cryo-EM to study the binding of a multivalent ligand to a lectin. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7oj7.cif.gz | 214.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oj7.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7oj7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7oj7_validation.pdf.gz | 722.1 KB | Display | wwPDB validaton report |
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Full document | 7oj7_full_validation.pdf.gz | 722.6 KB | Display | |
Data in XML | 7oj7_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 7oj7_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/7oj7 ftp://data.pdbj.org/pub/pdb/validation_reports/oj/7oj7 | HTTPS FTP |
-Related structure data
Related structure data | 4q4wS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Capsid protein ... , 4 types, 4 molecules 111222333444
#1: Protein | Mass: 34378.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coxsackievirus A24 / Strain: A24v / Production host: Homo sapiens (human) / References: UniProt: V9VEF3 |
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#2: Protein | Mass: 29817.412 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coxsackievirus A24 / Strain: A24v / Production host: Homo sapiens (human) / References: UniProt: V9VEF3 |
#3: Protein | Mass: 26637.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coxsackievirus A24 / Strain: A24v / Production host: Homo sapiens (human) / References: UniProt: V9VEF3 |
#4: Protein | Mass: 7319.045 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coxsackievirus A24 / Strain: A24v / Production host: Homo sapiens (human) / References: UniProt: V9VEF3 |
-Sugars , 1 types, 1 molecules
#7: Sugar | ChemComp-0H0 / |
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-Non-polymers , 3 types, 826 molecules
#5: Chemical | #6: Chemical | ChemComp-CL / #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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 / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 26, 2018 |
Radiation | Monochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→49.962 Å / Num. obs: 1921680 / % possible obs: 99.9 % / Redundancy: 7.7 % / Biso Wilson estimate: 22 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.263 / Rrim(I) all: 0.282 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 1.78→1.89 Å / Rmerge(I) obs: 1.331 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 308924 / CC1/2: 0.506 / Rrim(I) all: 1.428 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Q4W Resolution: 1.78→49.96 Å / Cor.coef. Fo:Fc: 0.97 / SU B: 2.14 / SU ML: 0.06 / Cross valid method: NONE / ESU R: 0.018 Details: Hydrogens have been added in their 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 PLUS MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.077 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→49.96 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Num. reflection Rfree: _ / Total num. of bins used: 20
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