[English] 日本語
Yorodumi- PDB-5o1z: Structure of Nrd1 RNA binding domain in complex with RNA (CGUAAA) -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o1z | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Nrd1 RNA binding domain in complex with RNA (CGUAAA) | ||||||
Components |
| ||||||
Keywords | TRANSCRIPTION / Nrd1 / RRM / RNA-binding / transcription non-coding RNAs / Nrd1 complex | ||||||
Function / homology | Function and homology information transcription regulatory region RNA binding / antisense RNA transcript catabolic process / Nrd1 complex / sno(s)RNA 3'-end processing / termination of RNA polymerase II transcription, exosome-dependent / snRNA 3'-end processing / tRNA 3'-end processing / CUT catabolic process / : / nuclear mRNA surveillance ...transcription regulatory region RNA binding / antisense RNA transcript catabolic process / Nrd1 complex / sno(s)RNA 3'-end processing / termination of RNA polymerase II transcription, exosome-dependent / snRNA 3'-end processing / tRNA 3'-end processing / CUT catabolic process / : / nuclear mRNA surveillance / mRNA 3'-end processing / protein domain specific binding / mRNA binding / RNA binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Franco-Echevarria, E. / Perez-Canadillas, J.M. / Gonzalez, B. | ||||||
Funding support | Spain, 1items
| ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2017 Title: The structure of transcription termination factor Nrd1 reveals an original mode for GUAA recognition. Authors: Franco-Echevarria, E. / Gonzalez-Polo, N. / Zorrilla, S. / Martinez-Lumbreras, S. / Santiveri, C.M. / Campos-Olivas, R. / Sanchez, M. / Calvo, O. / Gonzalez, B. / Perez-Canadillas, J.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5o1z.cif.gz | 51.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5o1z.ent.gz | 33.8 KB | Display | PDB format |
PDBx/mmJSON format | 5o1z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o1/5o1z ftp://data.pdbj.org/pub/pdb/validation_reports/o1/5o1z | HTTPS FTP |
---|
-Related structure data
Related structure data | 5o1tC 5o1wSC 5o1xC 5o1yC 5o20C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 20108.586 Da / Num. of mol.: 1 / Fragment: UNP residues 290-468 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: NRD1, YNL251C, N0868 / Production host: Escherichia coli (E. coli) / References: UniProt: P53617 |
---|---|
#2: RNA chain | Mass: 1899.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 66.88 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion / Details: 1M Sodium Potassium Phosphate pH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97929 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→59.69 Å / Num. obs: 5025 / % possible obs: 100 % / Redundancy: 23.9 % / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.033 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 3.4→3.67 Å / Redundancy: 25.2 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 8.5 / Num. unique all: 989 / Rpim(I) all: 0.116 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5O1W Resolution: 3.4→59.69 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.908 / SU B: 20.849 / SU ML: 0.307 / Cross valid method: THROUGHOUT / ESU R Free: 0.411 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 86.054 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.4→59.69 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|