|Entry||Database: PDB / ID: 2mow|
|Title||Structure of Nrd1p CID - Trf4p NIM complex|
|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 / termination of RNA polymerase II transcription, exosome-dependent / 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 ...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 / termination of RNA polymerase II transcription, exosome-dependent / 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 / RNA 3'-end processing / TRAMP complex / snRNA 3'-end processing / meiotic DNA double-strand break formation / nuclear polyadenylation-dependent CUT catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / tRNA 3'-end processing / nuclear polyadenylation-dependent tRNA catabolic process / nuclear polyadenylation-dependent rRNA catabolic process / CUT catabolic process / U4 snRNA 3'-end processing / RNA fragment catabolic process / RHOBTB1 GTPase cycle / polyadenylation-dependent snoRNA 3'-end processing / nuclear mRNA surveillance / histone mRNA catabolic process / poly(A) RNA polymerase activity / polynucleotide adenylyltransferase / tRNA modification / negative regulation of DNA recombination / mRNA 3'-end processing / 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
Nucleotidyltransferase Trf4-like / Nrd1/Seb1, RNA recognition motif / CID domain / RPR / CID domain / CID domain profile. / PAP/25A-associated / Cid1 family poly A polymerase / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / Polymerase, nucleotidyl transferase domain ...Nucleotidyltransferase Trf4-like / Nrd1/Seb1, RNA recognition motif / CID domain / RPR / CID domain / CID domain profile. / PAP/25A-associated / Cid1 family poly A polymerase / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / ENTH/VHS / Nucleotidyltransferase superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Nucleotide-binding alpha-beta plait domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Protein NRD1 / Poly(A) RNA polymerase protein 2
Similarity search - Component
|Biological species||Saccharomyces cerevisiae (baker'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.
|Structure viewer||Molecule: |
Downloads & links
A: Protein NRD1
B: Poly(A) RNA polymerase protein 2
|#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 (baker's yeast)
Gene: NRD1, YNL251C, N0868 / Plasmid: pET22b / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P53617
|#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 (baker's yeast) / References: UniProt: P53632
|Experiment||Method: SOLUTION NMR|
|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
|Sample conditions||Ionic strength: 0.1 / pH: 8.0 / Pressure: ambient / Temperature: 293.15 K|
|NMR software||Name: CYANA / Developer: Guntert, Mumenthaler and Wuthrich / Classification: refinement|
|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
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