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- PDB-5o1t: Solution structure of the RNA binding domain of Nrd1 -

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Basic information

Entry
Database: PDB / ID: 5o1t
TitleSolution structure of the RNA binding domain of Nrd1
ComponentsProtein NRD1
KeywordsRNA BINDING PROTEIN / Nrd1 / RRM / RNA-binding / transcription non-coding RNAs
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 / tRNA 3'-end processing / snRNA 3'-end processing / CUT catabolic process / nuclear mRNA surveillance / mRNA 3'-end processing ...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 / tRNA 3'-end processing / snRNA 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
: / Nrd1/Seb1, domain 2 / Nrd1/Seb1, RNA recognition motif / CID domain / RPR / CID domain / CID domain profile. / ENTH/VHS / RNA recognition motif / RNA recognition motif ...: / Nrd1/Seb1, domain 2 / Nrd1/Seb1, RNA recognition motif / CID domain / RPR / CID domain / CID domain profile. / ENTH/VHS / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / Minimization
AuthorsMartinez-Lumbreras, S. / Perez-Canadillas, J.M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spain
CitationJournal: 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
DepositionMay 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein NRD1


Theoretical massNumber of molelcules
Total (without water)20,0521
Polymers20,0521
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10010 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50target function
RepresentativeModel #1medoid

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Components

#1: Protein Protein NRD1


Mass: 20051.533 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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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic23D HNCA
141isotropic23D HNCO
151isotropic23D CBCA(CO)NH
161isotropic23D (H)CCH-TOCSY
172isotropic22D 1H-1H NOESY
1131isotropic23D 1H-15N NOESY
1143isotropic22D 1H-1H NOESY F1filtered
1154isotropic22D 1H-1H NOESY F1filtered
1165isotropic22D 1H-1H NOESY F1filtered

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution1600 uM [U-100% 13C; U-100% 15N] Nrd1, 25 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2ONrd1_CN90% H2O/10% D2O
solution2800 uM Nrd1, 25 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2ONrd1_na90% H2O/10% D2O
solution3400 uM [U-100% 13C; U-100% 15N] expect for Phe and Leu residues Nrd1, 25 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2ONrd1_PheLeu90% H2O/10% D2O13C 15N sample uniformly unlabelled in Phe and Leu (12C/14N)
solution4400 uM [U-100% 13C; U-100% 15N] expect for Ile residues Nrd1, 25 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2ONrd1_Ile90% H2O/10% D2O13C 15N sample uniformly unlabelled in Ile (12C/14N)
solution5400 uM [U-100% 13C; U-100% 15N] expect for Arg residues Nrd1, 25 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2ONrd1_Arg90% H2O/10% D2O13C 15N sample uniformly unlabelled in Arg (12C/14N)
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
600 uMNrd1[U-100% 13C; U-100% 15N]1
25 mMpotassium phosphatenatural abundance1
25 mMsodium chloridenatural abundance1
1 mMDTTnatural abundance1
800 uMNrd1natural abundance2
25 mMpotassium phosphatenatural abundance2
25 mMsodium chloridenatural abundance2
1 mMDTTnatural abundance2
400 uMNrd1[U-100% 13C; U-100% 15N] expect for Phe and Leu residues3
25 mMpotassium phosphatenatural abundance3
25 mMsodium chloridenatural abundance3
1 mMDTTnatural abundance3
400 uMNrd1[U-100% 13C; U-100% 15N] expect for Ile residues4
25 mMpotassium phosphatenatural abundance4
25 mMsodium chloridenatural abundance4
1 mMDTTnatural abundance4
400 uMNrd1[U-100% 13C; U-100% 15N] expect for Arg residues5
25 mMpotassium phosphatenatural abundance5
25 mMsodium chloridenatural abundance5
1 mMDTTnatural abundance5
Sample conditionsIonic strength: 59.1 mM / Label: Nrd1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: Minimization / Software ordinal: 5
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 20

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