[English] 日本語
Yorodumi- 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 | ||||||
Components |
| ||||||
Keywords | TRANSLATION/RNA / HDV / ribozyme / RNA / U1A / precurosr / TRANSLATION-RNA COMPLEX | ||||||
Function / homology | Function and homology information 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 | Hepatitis delta virus Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Ke, A. / Zhou, K. / Ding, F. / Cate, J.H. / Doudna, J.A. | ||||||
Citation | Journal: Nature / Year: 2004 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: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1sj3.cif.gz | 73.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1sj3.ent.gz | 52.6 KB | Display | PDB format |
PDBx/mmJSON format | 1sj3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sj/1sj3 ftp://data.pdbj.org/pub/pdb/validation_reports/sj/1sj3 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1sj4C 1sjfC 1vbxC 1vbyC 1vbzC 1vc0C 1vc5C 1vc6C C: citing same article (ref.) |
---|---|
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.) Hepatitis delta virus / Genus: Deltavirus / Description: C75U in vitro transcription / Plasmid: pUC19-pT3 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha | ||
---|---|---|---|
#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.) Homo sapiens (human) / Description: Y31H, Q36R; / Gene: SNRPA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P09012 | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-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: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9892 Å |
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: MOLECULAR REPLACEMENT / Resolution: 2.2→31.39 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2862606.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
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 |
|