+Open data
-Basic information
Entry | Database: PDB / ID: 4j1g | ||||||
---|---|---|---|---|---|---|---|
Title | Leanyer orthobunyavirus nucleoprotein-ssRNA complex | ||||||
Components |
| ||||||
Keywords | VIRAL PROTEIN/RNA / PROTEIN-RNA COMPLEX / RNA binding protein / RNA binding / nucleocapsid protein / VIRAL PROTEIN-RNA complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Leanyer virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.789 Å | ||||||
Authors | Niu, F. / Shaw, N. / Wang, Y. / Jiao, L. / Ding, W. / Li, X. / Zhu, P. / Upur, H. / Ouyang, S. / Cheng, G. / Liu, Z.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Structure of the Leanyer orthobunyavirus nucleoprotein-RNA complex reveals unique architecture for RNA encapsidation. Authors: Niu, F. / Shaw, N. / Wang, Y.E. / Jiao, L. / Ding, W. / Li, X. / Zhu, P. / Upur, H. / Ouyang, S. / Cheng, G. / Liu, Z.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4j1g.cif.gz | 207.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4j1g.ent.gz | 168.7 KB | Display | PDB format |
PDBx/mmJSON format | 4j1g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4j1g_validation.pdf.gz | 479.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4j1g_full_validation.pdf.gz | 532.1 KB | Display | |
Data in XML | 4j1g_validation.xml.gz | 41.1 KB | Display | |
Data in CIF | 4j1g_validation.cif.gz | 56.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/4j1g ftp://data.pdbj.org/pub/pdb/validation_reports/j1/4j1g | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 26295.250 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leanyer virus / Production host: Escherichia coli (E. coli) / References: UniProt: F2WAD7 #2: RNA chain | | Mass: 13732.498 Da / Num. of mol.: 1 / Source method: obtained synthetically #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 44.98 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1-0.2 mM ammonium citrate tribasic (pH 7.0) and 15 - 18% (w/v) PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 13, 2012 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.78→48.047 Å / Num. all: 25492 / Num. obs: 23912 / % possible obs: 93.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.78→2.88 Å / % possible all: 69 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.789→48.047 Å / SU ML: 0.41 / σ(F): 1.99 / Phase error: 34.47 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.789→48.047 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|