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- PDB-2mow: Structure of Nrd1p CID - Trf4p NIM complex -

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Basic information

Entry
Database: PDB / ID: 2mow
TitleStructure of Nrd1p CID - Trf4p NIM complex
Components
  • Poly(A) RNA polymerase protein 2
  • Protein NRD1
KeywordsTRANSCRIPTION / transcription termination / RNA degradation / RNAP II CTD / protein-protein interaction
Function / homology
Function and homology information


polyadenylation-dependent ncRNA catabolic process / polyadenylation-dependent mRNA catabolic process / transcription regulatory region RNA binding / antisense RNA transcript catabolic process / Nrd1 complex / RNA 3'-end processing / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / termination of RNA polymerase II transcription, exosome-dependent / sno(s)RNA 3'-end processing ...polyadenylation-dependent ncRNA catabolic process / polyadenylation-dependent mRNA catabolic process / transcription regulatory region RNA binding / antisense RNA transcript catabolic process / Nrd1 complex / RNA 3'-end processing / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / termination of RNA polymerase II transcription, exosome-dependent / sno(s)RNA 3'-end processing / TRAMP complex / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / meiotic DNA double-strand break formation / nuclear mRNA surveillance of mRNA 3'-end processing / RNA fragment catabolic process / nuclear polyadenylation-dependent CUT catabolic process / tRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / CUT catabolic process / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / snRNA 3'-end processing / poly(A)-dependent snoRNA 3'-end processing / histone mRNA catabolic process / nuclear mRNA surveillance / negative regulation of DNA recombination / polynucleotide adenylyltransferase / tRNA modification / poly(A) RNA polymerase activity / mRNA 3'-end processing / 5'-deoxyribose-5-phosphate lyase activity / base-excision repair / protein domain specific binding / cell division / mRNA binding / nucleolus / RNA binding / ATP binding / nucleus / metal ion binding / cytosol
Similarity search - Function
Nucleotidyltransferase Trf4-like / : / Nrd1/Seb1, domain 2 / Nrd1/Seb1, RNA recognition motif / CID domain / RPR / CID domain / CID domain profile. / PAP/25A-associated / Cid1 family poly A polymerase ...Nucleotidyltransferase Trf4-like / : / Nrd1/Seb1, domain 2 / 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 / Poly(A) RNA polymerase, mitochondrial-like, central palm domain / ENTH/VHS / Nucleotidyltransferase superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / RNA-binding domain superfamily / 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 speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model9
AuthorsKabzinski, T. / Stefl, R. / Kubicek, K.
CitationJournal: 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
DepositionMay 6, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein NRD1
B: Poly(A) RNA polymerase protein 2


Theoretical massNumber of molelcules
Total (without water)19,7322
Polymers19,7322
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein NRD1 / Nrd1p


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
#2: Protein/peptide Poly(A) RNA polymerase protein 2 / Trf4p / DNA polymerase kappa / DNA polymerase sigma / Topoisomerase 1-related protein TRF4


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CO)CA
1413D HBHA(CO)NH
1513D 1H-15N NOESY
1613D 1H-13C NOESY
1713D F1-13C/15N-filtered NOESY-[13C,1H]-HSQC
1812D F1, F2-13C/15N-filtered [1H,1H]-NOESY

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Sample preparation

DetailsContents: 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
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMTrf4p-11
1 mMNrd1p-2[U-99% 13C; U-99% 15N]1
100 mMsodium chloride-31
50 mMsodium phosphate-41
Sample conditionsIonic strength: 0.1 / pH: 8 / Pressure: ambient / Temperature: 293.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9501
Bruker AvanceBrukerAVANCE7002

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Processing

NMR softwareName: CYANA / Developer: Guntert, Mumenthaler and Wuthrich / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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