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Yorodumi- PDB-4jgy: Crystal structure of human coxsackievirus A16 uncoating intermedi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jgy | ||||||
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Title | Crystal structure of human coxsackievirus A16 uncoating intermediate (space group P4232) | ||||||
Components |
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Keywords | VIRUS / hand-foot-and-mouth disease / picornavirus uncoating / pocket factor / icosahedral virus | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / 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 ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / 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 / 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 / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Human coxsackievirus A16 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Ren, J. / Wang, X. / Hu, Z. / Gao, Q. / Sun, Y. / Li, X. / Porta, C. / Walter, T.S. / Gilbert, R.J. / Zhao, Y. ...Ren, J. / Wang, X. / Hu, Z. / Gao, Q. / Sun, Y. / Li, X. / Porta, C. / Walter, T.S. / Gilbert, R.J. / Zhao, Y. / Axford, D. / Williams, M. / Mcauley, K. / Rowlands, D.J. / Yin, W. / Wang, J. / Stuart, D.I. / Rao, Z. / Fry, E.E. | ||||||
Citation | Journal: Nat Commun / Year: 2013 Title: Picornavirus uncoating intermediate captured in atomic detail. Authors: Ren, J. / Wang, X. / Hu, Z. / Gao, Q. / Sun, Y. / Li, X. / Porta, C. / Walter, T.S. / Gilbert, R.J. / Zhao, Y. / Axford, D. / Williams, M. / McAuley, K. / Rowlands, D.J. / Yin, W. / Wang, J. ...Authors: Ren, J. / Wang, X. / Hu, Z. / Gao, Q. / Sun, Y. / Li, X. / Porta, C. / Walter, T.S. / Gilbert, R.J. / Zhao, Y. / Axford, D. / Williams, M. / McAuley, K. / Rowlands, D.J. / Yin, W. / Wang, J. / Stuart, D.I. / Rao, Z. / Fry, E.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jgy.cif.gz | 150.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jgy.ent.gz | 118.4 KB | Display | PDB format |
PDBx/mmJSON format | 4jgy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jgy_validation.pdf.gz | 447.4 KB | Display | wwPDB validaton report |
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Full document | 4jgy_full_validation.pdf.gz | 463.7 KB | Display | |
Data in XML | 4jgy_validation.xml.gz | 26.7 KB | Display | |
Data in CIF | 4jgy_validation.cif.gz | 35.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/4jgy ftp://data.pdbj.org/pub/pdb/validation_reports/jg/4jgy | HTTPS FTP |
-Related structure data
Related structure data | 4jgzC 3vbrS 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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2 |
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3 |
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4 |
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5 |
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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
#1: Protein | Mass: 33090.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GROWN IN VERO CELLS / Source: (natural) Human coxsackievirus A16 / Strain: Ningbo.CHN/028-2/2009 / References: UniProt: I3W9E1 |
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#2: Protein | Mass: 27587.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GROWN IN VERO CELLS / Source: (natural) Human coxsackievirus A16 / Strain: Ningbo.CHN/028-2/2009 / References: UniProt: I3W9E1 |
#3: Protein | Mass: 26654.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GROWN IN VERO CELLS / Source: (natural) Human coxsackievirus A16 / Strain: Ningbo.CHN/028-2/2009 / References: UniProt: I3W9E1 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 32 |
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-Sample preparation
Crystal | Density Matthews: 4.38 Å3/Da / Density % sol: 71.94 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.88 M lithium sulfate monohydrate, 0.1 M BIS-TRIS propane, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 3→50 Å / Num. obs: 150962 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 61.4 Å2 / Rmerge(I) obs: 0.604 / Net I/σ(I): 2.8 | |||||||||||||||
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 0.3 / Num. unique all: 13824 / % possible all: 91.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3VBR Resolution: 3→49.51 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 19783238.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.1135 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→49.51 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.11 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 10
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Xplor file |
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