[English] 日本語
![](img/lk-miru.gif)
- PDB-1sj3: Hepatitis Delta Virus Gemonic Ribozyme Precursor, with Mg2+ Bound -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1sj3 | ||||||
---|---|---|---|---|---|---|---|
Title | Hepatitis Delta Virus Gemonic Ribozyme Precursor, with Mg2+ Bound | ||||||
![]() |
| ||||||
![]() | TRANSLATION/RNA / HDV / ribozyme / RNA / U1A / precurosr / TRANSLATION-RNA COMPLEX | ||||||
Function / homology | ![]() U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm ...U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ke, A. / Zhou, K. / Ding, F. / Cate, J.H. / Doudna, J.A. | ||||||
![]() | ![]() Title: A Conformational Switch controls hepatitis delta virus ribozyme catalysis Authors: Ke, A. / Zhou, K. / Ding, F. / Cate, J.H. / Doudna, J.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 73.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 52.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 463.3 KB | Display | |
Data in XML | ![]() | 9.2 KB | Display | |
Data in CIF | ![]() | 12.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1sj4C ![]() 1sjfC ![]() 1vbxC ![]() 1vbyC ![]() 1vbzC ![]() 1vc0C ![]() 1vc5C ![]() 1vc6C C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
| ||||||||||
Components on special symmetry positions |
|
-
Components
#1: RNA chain | Mass: 24467.521 Da / Num. of mol.: 1 / Mutation: C75U Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
---|---|---|---|
#2: Protein | Mass: 11498.472 Da / Num. of mol.: 1 / Fragment: RNA binding domain / Mutation: Y31H, Q36R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.5 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: NaCl, MgCl2, MPD, Sodium Cacodylate, Spermine-HCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 80 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 29, 2003 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9892 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→34 Å / Num. all: 22445 / Num. obs: 21056 / % possible obs: 0.938 % / Observed criterion σ(I): 2.5 / Biso Wilson estimate: 30.2 Å2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.6652 Å2 / ksol: 0.393894 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.8 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→31.39 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|