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- PDB-5tpy: Crystal structure of an exonuclease resistant RNA from Zika virus -
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Open data
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Basic information
Entry | Database: PDB / ID: 5tpy | ||||||
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Title | Crystal structure of an exonuclease resistant RNA from Zika virus | ||||||
![]() | RNA (71-MER) | ||||||
![]() | RNA / Zika RNA exonuclease resistance | ||||||
Function / homology | HEXANE-1,6-DIOL / RNA / RNA (> 10)![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Akiyama, B.M. / Laurence, H.M. / Massey, A.R. / Costantino, D.A. / Xie, X. / Yang, Y. / Shi, P.-Y. / Nix, J.C. / Beckham, J.D. / Kieft, J.S. | ||||||
![]() | ![]() Title: Zika virus produces noncoding RNAs using a multi-pseudoknot structure that confounds a cellular exonuclease. Authors: Akiyama, B.M. / Laurence, H.M. / Massey, A.R. / Costantino, D.A. / Xie, X. / Yang, Y. / Shi, P.Y. / Nix, J.C. / Beckham, J.D. / Kieft, J.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.9 KB | Display | ![]() |
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PDB format | ![]() | 35.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 404.2 KB | Display | ![]() |
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Full document | ![]() | 405 KB | Display | |
Data in XML | ![]() | 4.3 KB | Display | |
Data in CIF | ![]() | 5.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4pqvS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: RNA chain | Mass: 23017.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: MR766-NIID / Source: (synth.) ![]() ![]() |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-HEZ / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.55 Å3/Da / Density % sol: 65.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: drop: 1 uL 5 mg/mL RNA in 2.5 mM magnesium chloride, 10 mM HEPES-KOH pH 7.5 (heated to 65 C for 3 minutes, cooled at room temperature, 0.5 mM spermidine added, centrifuged for 10 minutes at ...Details: drop: 1 uL 5 mg/mL RNA in 2.5 mM magnesium chloride, 10 mM HEPES-KOH pH 7.5 (heated to 65 C for 3 minutes, cooled at room temperature, 0.5 mM spermidine added, centrifuged for 10 minutes at 13000 x g) + 1 uL 50 mM sodium cacodylate pH 6.0, 150 mM NaCl, 4 mM CaCl2, 0.6 mM spermine, 36% 1,6-hexanediol. Crystals were flash-frozen in the mother liquor using liquid nitrogen for x-ray diffraction. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Mar 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0972 Å / Relative weight: 1 |
Reflection | Resolution: 2.805→55.839 Å / Num. obs: 15501 / % possible obs: 99.6 % / Redundancy: 21.1 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 31.5 |
Reflection shell | Resolution: 2.81→2.91 Å / Redundancy: 21.1 % / Rmerge(I) obs: 1.492 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.82 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4pqv Resolution: 2.805→55.839 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.805→55.839 Å
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Refine LS restraints |
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LS refinement shell |
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