|Entry||Database: PDB / ID: 2m88|
|Title||NMR structure of a two-domain RNA-binding fragment of Nrd1|
|Keywords||RNA BINDING PROTEIN / Nrd1 complex / RNA processing and degradation / RRM structure|
|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 / RHOBTB1 GTPase cycle / 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 / RHOBTB1 GTPase cycle / CUT catabolic process / nuclear mRNA surveillance / mRNA 3'-end processing / termination of RNA polymerase II transcription / protein domain specific binding / mRNA binding / RNA binding / nucleus
Similarity search - Function
Nrd1/Seb1, RNA recognition motif / CID domain / RPR / CID domain / CID domain profile. / ENTH/VHS / RRM (RNA recognition motif) domain / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...Nrd1/Seb1, RNA recognition motif / CID domain / RPR / CID domain / CID domain profile. / ENTH/VHS / RRM (RNA recognition motif) domain / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Similarity search - Component
|Biological species||Saccharomyces cerevisiae (baker's yeast)|
|Method||SOLUTION NMR / torsion angle dynamics, simulated annealing, molecular dynamics, simulated annealing|
|Model details||lowest energy, model1|
|Authors||Bacikova, V. / Pasulka, J. / Kubicek, K. / Stefl, R.|
|Citation||Journal: Nucleic Acids Res. / Year: 2014|
Title: Structure and semi-sequence-specific RNA binding of Nrd1.
Authors: Bacikova, V. / Pasulka, J. / Kubicek, K. / Stefl, R.
|Structure viewer||Molecule: |
-Downloads & links
|PDBx/mmCIF format||2m88.cif.gz||1.1 MB||Display||PDBx/mmCIF format|
|PDB format||pdb2m88.ent.gz||975.7 KB||Display||PDB format|
|PDBx/mmJSON format||2m88.json.gz||Tree view||PDBx/mmJSON format|
|Summary document||2m88_validation.pdf.gz||342.9 KB||Display||wwPDB validaton report|
|Full document||2m88_full_validation.pdf.gz||488.5 KB||Display|
|Data in XML||2m88_validation.xml.gz||74.4 KB||Display|
-Related structure data
|Similar structure data|
|PDB pages||PDBj / wwPDB / NCBI|
|Related items in Molecule of the Month|
A: Protein NRD1
|#1: Protein|| |
Mass: 21799.605 Da / Num. of mol.: 1 / Fragment: UNP residues 307-491
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: NRD1, YNL251C, N0868 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: P53617
|Experiment||Method: SOLUTION NMR|
Details: The structure was solved using ILV-protonated sample on a highly deuterated background
|Refinement||Method: torsion angle dynamics, simulated annealing, molecular dynamics, 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: 80 / Conformers submitted total number: 20
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