+Open data
-Basic information
Entry | Database: PDB / ID: 2mow | ||||||
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Title | Structure of Nrd1p CID - Trf4p NIM complex | ||||||
Components |
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Keywords | TRANSCRIPTION / transcription termination / RNA degradation / RNAP II CTD / protein-protein interaction | ||||||
Function / homology | Function and homology information polyadenylation-dependent mRNA catabolic process / transcription regulatory region RNA binding / antisense RNA transcript catabolic process / Nrd1 complex / nuclear mRNA surveillance of mRNA 3'-end processing / sno(s)RNA 3'-end processing / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / termination of RNA polymerase II transcription, exosome-dependent ...polyadenylation-dependent mRNA catabolic process / transcription regulatory region RNA binding / antisense RNA transcript catabolic process / Nrd1 complex / nuclear mRNA surveillance of mRNA 3'-end processing / sno(s)RNA 3'-end processing / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / termination of RNA polymerase II transcription, exosome-dependent / TRAMP complex / meiotic DNA double-strand break formation / snRNA 3'-end processing / tRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / RNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / RNA fragment catabolic process / CUT catabolic process / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / : / poly(A)-dependent snoRNA 3'-end processing / polynucleotide adenylyltransferase / histone mRNA catabolic process / poly(A) RNA polymerase activity / nuclear mRNA surveillance / negative regulation of DNA recombination / mRNA 3'-end processing / tRNA modification / 5'-deoxyribose-5-phosphate lyase activity / localization / base-excision repair / cell division / protein domain specific binding / mRNA binding / nucleolus / RNA binding / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model9 | ||||||
Authors | Kabzinski, T. / Stefl, R. / Kubicek, K. | ||||||
Citation | Journal: Mol.Cell / Year: 2014 Title: Molecular Basis for Coordinating Transcription Termination with Noncoding RNA Degradation. Authors: Tudek, A. / Porrua, O. / Kabzinski, T. / Lidschreiber, M. / Kubicek, K. / Fortova, A. / Lacroute, F. / Vanacova, S. / Cramer, P. / Stefl, R. / Libri, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2mow.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2mow.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 2mow.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mo/2mow ftp://data.pdbj.org/pub/pdb/validation_reports/mo/2mow | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 18315.674 Da / Num. of mol.: 1 / Fragment: CID (UNP residues 1-153) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: NRD1, YNL251C, N0868 / Plasmid: pET22b / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53617 |
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#2: Protein/peptide | Mass: 1416.359 Da / Num. of mol.: 1 / Fragment: NIM (UNP residues 573-584) / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53632 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.5 mM Trf4p, 1 mM [U-99% 13C; U-99% 15N] Nrd1p, 100 mM sodium chloride, 50 mM sodium phosphate, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.1 / pH: 8.0 / Pressure: ambient / Temperature: 293.15 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software | Name: CYANA / Developer: Guntert, Mumenthaler and Wuthrich / Classification: refinement |
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Refinement | Method: simulated annealing / Software ordinal: 1 |
NMR representative | Selection criteria: lowest energy |
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |