BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 11523

Title: Solution structure of the second RRM domain of Nrd1   PubMed: 23770370

Deposition date: 2013-04-16 Original release date: 2014-04-14

Authors: Kobayashi, Ayaho; Kanaba, Teppei; Mishima, Masaki

Citation: Kobayashi, Ayaho; Kanaba, Teppei; Satoh, Ryosuke; Fujiwara, Toshinobu; Ito, Yutaka; Sugiura, Reiko; Mishima, Masaki. "Structure of the second RRM domain of Nrd1, a fission yeast MAPK target RNA binding protein, and implication for its RNA recognition and regulation"  Biochem. Biophys. Res. Commun. 437, 12-17 (2013).

Assembly members:
Nrd1_RRM2, polymer, 97 residues, 10793.440 Da.

Natural source:   Common Name: fission yeast   Taxonomy ID: 4896   Superkingdom: Eukaryota   Kingdom: Fungi   Genus/species: Schizosaccharomyces pombe

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET-49b(+)

Entity Sequences (FASTA):
Nrd1_RRM2: NSASNSSVLLAVQQSGACRN VFLGNLPNGITEDEIREDLE PFGPIDQIKIVTERNIAFVH FLNIAAAIKAVQELPLNPKW SKRRIYYGRDRCAVGLK

Data sets:
Data typeCount
13C chemical shifts410
15N chemical shifts93
1H chemical shifts652

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1Nrd1_RRM21

Entities:

Entity 1, Nrd1_RRM2 97 residues - 10793.440 Da.

1   ASNSERALASERASNSERSERVALLEULEU
2   ALAVALGLNGLNSERGLYALACYSARGASN
3   VALPHELEUGLYASNLEUPROASNGLYILE
4   THRGLUASPGLUILEARGGLUASPLEUGLU
5   PROPHEGLYPROILEASPGLNILELYSILE
6   VALTHRGLUARGASNILEALAPHEVALHIS
7   PHELEUASNILEALAALAALAILELYSALA
8   VALGLNGLULEUPROLEUASNPROLYSTRP
9   SERLYSARGARGILETYRTYRGLYARGASP
10   ARGCYSALAVALGLYLEULYS

Samples:

sample_1: potassium phosphate 50 mM; sodium chloride 100 mM; TCEP 1 mM; EDTA 0.1 mM; Nrd1 RRM2, [U-99% 13C; U-99% 15N], 1.0 mM; H2O 93%; D2O 7%

sample_2: potassium phosphate 50 mM; sodium chloride 100 mM; TCEP 1 mM; EDTA 0.1 mM; Nrd1 RRM2, [U-99% 15N], 1.2 mM; H2O 93%; D2O 7%

sample_3: potassium phosphate 50 mM; sodium chloride 100 mM; TCEP 1 mM; EDTA 0.1 mM; Nrd1 RRM2, [U-99% 13C; U-99% 15N], 1.0 mM; D2O 100%

sample_4: potassium phosphate 50 mM; sodium chloride 100 mM; TCEP 1 mM; EDTA 0.1 mM; Nrd1 RRM2, [U-10% 13C; U-99% 15N], 0.35 mM; H2O 93%; D2O 7%

sample_conditions_1: pH: 6.0; pressure: 1 atm; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
4D H(CCO)NHsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_3isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D HNHBsample_2isotropicsample_conditions_1
3D HA(CA)HBsample_3isotropicsample_conditions_1
2D 1H-13C CT-HSQCsample_4isotropicsample_conditions_1

Software:

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

SPARKY, Goddard - chemical shift assignment

TALOS, Cornilescu, Delaglio and Bax - data analysis

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

TOPSPIN, Bruker Biospin - collection

NMR spectrometers:

  • Bruker AvanceIII 600 MHz

Related Database Links:

PDB

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts