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Yorodumi- PDB-5o20: Structure of Nrd1 RNA binding domain in complex with RNA (UUAGUAAUCC) -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o20 | ||||||||||||
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Title | Structure of Nrd1 RNA binding domain in complex with RNA (UUAGUAAUCC) | ||||||||||||
Components |
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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: 3.53 Å | ||||||||||||
Authors | Franco-Echevarria, E. / Perez-Canadillas, J.M. / Gonzalez, B. | ||||||||||||
Funding support | Spain, 3items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o20.cif.gz | 47.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o20.ent.gz | 34.6 KB | Display | PDB format |
PDBx/mmJSON format | 5o20.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/5o20 ftp://data.pdbj.org/pub/pdb/validation_reports/o2/5o20 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20108.586 Da / Num. of mol.: 1 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 |
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#2: RNA chain | Mass: 3122.893 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) |
#3: Chemical | ChemComp-TRS / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 66.71 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / Details: 1M Sodium Potassium Phosphate pH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 3.53→60.96 Å / Num. obs: 4716 / % possible obs: 99.5 % / Redundancy: 9.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.081 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 3.53→3.87 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1077 / CC1/2: 0.99 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.53→60.96 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.897 / SU B: 31.962 / SU ML: 0.441 / Cross valid method: THROUGHOUT / ESU R Free: 0.552 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 122.488 Å2
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Refinement step | Cycle: 1 / Resolution: 3.53→60.96 Å
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Refine LS restraints |
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