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- PDB-1kh6: Crystal Structure of an RNA Tertiary Domain Essential to HCV IRES... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kh6 | ||||||
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Title | Crystal Structure of an RNA Tertiary Domain Essential to HCV IRES-mediated Translation Initiation. | ||||||
![]() | JIIIabc | ||||||
![]() | RNA / translation / RNA structure / IRES / HCV / bromine / four-way junction | ||||||
Function / homology | RNA / RNA (> 10)![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kieft, J.S. / Zhou, K. / Grech, A. / Jubin, R. / Doudna, J.A. | ||||||
![]() | ![]() Title: Crystal structure of an RNA tertiary domain essential to HCV IRES-mediated translation initiation. Authors: Kieft, J.S. / Zhou, K. / Grech, A. / Jubin, R. / Doudna, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 34.2 KB | Display | ![]() |
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PDB format | ![]() | 25.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 401.9 KB | Display | ![]() |
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Full document | ![]() | 402.9 KB | Display | |
Data in XML | ![]() | 4.1 KB | Display | |
Data in CIF | ![]() | 4.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: RNA chain | Mass: 17634.660 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The sequence is from Hepatitis C virus genotype 1B. In Vitro Transcription. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.1 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 30% MPD, 0.1 M sodium citrate pH 5.6, 0.2 M ammonium acetate, 2.5 mM magnesium chloride, and 1 mM spermidine, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 303K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 5.6 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.8→50 Å / Num. obs: 9652 / Observed criterion σ(I): 0 | |||||||||||||||
Reflection | *PLUS Lowest resolution: 50 Å / % possible obs: 98.3 % / Num. measured all: 72167 / Rmerge(I) obs: 0.078 | |||||||||||||||
Reflection shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 95.1 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 2.5 |
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Processing
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Refinement | Resolution: 2.9→50 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.9→50 Å
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Refinement | *PLUS Lowest resolution: 50 Å / Rfactor obs: 0.279 / Rfactor Rfree: 0.283 / Rfactor Rwork: 0.279 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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