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Open data
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Basic information
Entry | Database: PDB / ID: 1nd2 | ||||||
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Title | The structure of Rhinovirus 16 | ||||||
![]() | (coat protein ...) x 4 | ||||||
![]() | VIRUS / HRV 16 / rhinovirus / piconaviridae / pocket factor / Icosahedral virus | ||||||
Function / homology | ![]() symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / 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 / 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 RIG-I activity / 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 / 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 / DNA replication / 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 / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zhang, Y. / Simpson, A.A. / Bator, C.M. / Chakravarty, S. / Pevear, D.C. / Skochko, G.A. / Tull, T.M. / Diana, G. / Rossmann, M.G. | ||||||
![]() | ![]() Title: Structural and virological studies of the stages of virus replication that are affected by antirhinovirus compounds Authors: Zhang, Y. / Simpson, A.A. / Ledford, R.M. / Bator, C.M. / Chakravarty, S. / Skochko, G.A. / Demenczuk, T.M. / Watanyar, A. / Pevear, D.C. / Rossmann, M.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 180.5 KB | Display | ![]() |
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PDB format | ![]() | 141.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 395.2 KB | Display | ![]() |
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Full document | ![]() | 403.9 KB | Display | |
Data in XML | ![]() | 17.8 KB | Display | |
Data in CIF | ![]() | 29.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 |
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3 | ![]()
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4 | ![]()
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5 | ![]()
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Unit cell |
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Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) |
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Components
-Coat protein ... , 4 types, 4 molecules ABCD
#1: Protein | Mass: 32501.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 28990.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: Protein | Mass: 26314.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#4: Protein | Mass: 7374.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 3 types, 496 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MYR.gif)
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#5: Chemical | ChemComp-ZN / | ||
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#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
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Components of the solutions | *PLUS
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 710094 / Observed criterion σ(I): 0 |
Reflection | *PLUS % possible obs: 52.3 % / Num. measured all: 1294215 / Rmerge(I) obs: 0.038 |
Reflection shell | *PLUS % possible obs: 20.9 % / Rmerge(I) obs: 0.081 |
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Processing
Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints | *PLUS
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