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- PDB-2m88: NMR structure of a two-domain RNA-binding fragment of Nrd1 -

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Basic information

Entry
Database: PDB / ID: 2m88
TitleNMR structure of a two-domain RNA-binding fragment of Nrd1
ComponentsProtein NRD1
KeywordsRNA 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 / termination of RNA polymerase II transcription, exosome-dependent / sno(s)RNA 3'-end processing / tRNA 3'-end processing / CUT catabolic process / snRNA 3'-end processing / nuclear mRNA surveillance / mRNA 3'-end processing ...transcription regulatory region RNA binding / antisense RNA transcript catabolic process / Nrd1 complex / termination of RNA polymerase II transcription, exosome-dependent / sno(s)RNA 3'-end processing / tRNA 3'-end processing / CUT catabolic process / snRNA 3'-end processing / 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 / RRM (RNA recognition motif) domain / RNA recognition motif ...: / Nrd1/Seb1, domain 2 / Nrd1/Seb1, RNA recognition motif / CID domain / RPR / CID domain / CID domain profile. / ENTH/VHS / RRM (RNA recognition motif) domain / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing, molecular dynamics, simulated annealing
Model detailslowest energy, model1
AuthorsBacikova, V. / Pasulka, J. / Kubicek, K. / Stefl, R.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Structure and semi-sequence-specific RNA binding of Nrd1.
Authors: Bacikova, V. / Pasulka, J. / Kubicek, K. / Stefl, R.
History
DepositionMay 8, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Jul 9, 2014Group: Database references
Revision 1.3Jul 16, 2014Group: Database references
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.5May 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


Theoretical massNumber of molelcules
Total (without water)21,8001
Polymers21,8001
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 / 80structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein NRD1


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 (brewer's yeast)
Gene: NRD1, YNL251C, N0868 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: P53617

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: The structure was solved using ILV-protonated sample on a highly deuterated background
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CO)CA
1413D HN(CA)CB
1513D HN(COCA)CB
2622D 1H-15N HSQC
2723D HNCO
2823D HCACO
3934D (H)CCH methyl NOESY
31033D (H)CC(CO)NH
31133D CCH TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM [U-13C; U-15N] Nrd1, 50 mM sodium phosphate, 300 mM sodium chloride, 10 mM beta-mercaptoethanol, 90% H2O/10% D2O90% H2O/10% D2O
20.4 mM [U-100% 13C; U-100% 15N; U-80% 2H] Nrd1, 50 mM sodium phosphate, 300 mM sodium chloride, 10 mM beta-mercaptoethanol, 90% H2O/10% D2O90% H2O/10% D2O
30.4 mM [U-13C; U-15N; U-2H] Nrd1, 50 mM sodium phosphate, 300 mM sodium chloride, 10 mM beta-mercaptoethanol, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMNrd1-1[U-13C; U-15N]1
50 mMsodium phosphate-21
300 mMsodium chloride-31
10 mMbeta-mercaptoethanol-41
0.4 mMNrd1-5[U-100% 13C; U-100% 15N; U-80% 2H]2
50 mMsodium phosphate-62
300 mMsodium chloride-72
10 mMbeta-mercaptoethanol-82
0.4 mMNrd1-9[U-13C; U-15N; U-2H]3
50 mMsodium phosphate-103
300 mMsodium chloride-113
10 mMbeta-mercaptoethanol-123
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
18ambient 293 K
28ambient 293 K
38ambient 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE9503
Bruker AvanceBrukerAVANCE9004

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardpeak picking
SparkyGoddardnmr spectra analysis
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntonquality validation
WHAT IFVriendquality validation
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
MOLMOLKoradi, Billeter and Wuthrichvisualization
TopSpinBruker Biospinprocessing
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, simulated annealing, molecular dynamics, simulated annealing
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 80 / Conformers submitted total number: 20

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