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 11407

Title: Assigned chemical shifts of RNA binding domain 3 in RNA (UAUAUA)   PubMed: 19553194

Deposition date: 2010-09-09 Original release date: 2011-06-24

Authors: Tsuda, K.; Kuwasako, K.; Takahashi, M.; Someya, T.; Inoue, M.; Terada, T.; Kobayashi, N.; Shirouzu, M.; Kigawa, T.; Guntert, P.; Muto, Y.; Yokoyama, S.

Citation: Tsuda, Kengo; Kuwasako, Kanako; Takahashi, Mari; Someya, Tatsuhiko; Inoue, Makoto; Terada, Takaho; Kobayashi, Naohiro; Shirouzu, Mikako; Kigawa, Takanori; Tanaka, Akiko; Sugano, Sumio; Guntert, Peter; Muto, Yutaka; Yokoyama, Shigeyuki. "Structural basis for the sequence-specific RNA-recognition mechanism of human CUG-BP1 RRM3."  Nucleic Acids Res. 37, 5151-5166 (2009).

Assembly members:
RNA recognition motif, polymer, 115 residues, Formula weight is not available
RNA (UAUAUA), polymer, 6 residues, Formula weight is not available

Natural source:   Common Name: human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:   Production method: cell free synthesis   Host organism: E. coli - cell free

Entity Sequences (FASTA):
RNA recognition motif: GSSGSSGLTQQSIGAAGSQK EGPEGANLFIYHLPQEFGDQ DLLQMFMPFGNVVSAKVFID KQTNLSKCFGFVSYDNPVSA QAAIQSMNGFQIGMKRLKVQ LKRSKNDSKSGPSSG
RNA (UAUAUA): UAUAUA

Data sets:
Data typeCount
15N chemical shifts100
1H chemical shifts100

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1RNA recognition motif1
2RNA (UAUAUA)2

Entities:

Entity 1, RNA recognition motif 115 residues - Formula weight is not available

1   GLYSERSERGLYSERSERGLYLEUTHRGLN
2   GLNSERILEGLYALAALAGLYSERGLNLYS
3   GLUGLYPROGLUGLYALAASNLEUPHEILE
4   TYRHISLEUPROGLNGLUPHEGLYASPGLN
5   ASPLEULEUGLNMETPHEMETPROPHEGLY
6   ASNVALVALSERALALYSVALPHEILEASP
7   LYSGLNTHRASNLEUSERLYSCYSPHEGLY
8   PHEVALSERTYRASPASNPROVALSERALA
9   GLNALAALAILEGLNSERMETASNGLYPHE
10   GLNILEGLYMETLYSARGLEULYSVALGLN
11   LEULYSARGSERLYSASNASPSERLYSSER
12   GLYPROSERSERGLY

Entity 2, RNA (UAUAUA) 6 residues - Formula weight is not available

1   UAUAUA

Samples:

sample_1: RNA recognition motif, [U-13C; U-15N], 0.2 mM; RNA (UAUAUA) 0.4 mM; salt 100 mM; H2O 90%; D2O 10%

condition_1: ionic strength: 120 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
3D 1H-15N NOESYsample_1isotropiccondition_1
3D 1H-13C NOESYsample_1isotropiccondition_1

Software:

AMBER v9.0, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

xwinnmr v3.5, Bruker, Biospin - collection

NMRPipe v20030801, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer, and, Bax - processing

NMRView v5.0.4, Johnson, One, Moon, Scientific - data analysis

Kujira v0.9297, Kobayashi, N. - data analysis

CYANA v2.0.17, Guntert, Mumenthaler, and, Wuthrich - structure solution

NMR spectrometers:

  • Bruker Avance 700 MHz

Related Database Links:

BMRB 11405 11406 11408
PDB
DBJ BAB29392 BAE06101 BAE22391 BAE25504 BAE33820
EMBL CAC20566 CAC20707 CAH65197 CAH91665 CAJ82289
GB AAC50895 AAF78955 AAF78956 AAF78957 AAF86230
REF NP_001012539 NP_001017152 NP_001020592 NP_001020767 NP_001094682
SP P28659 Q28HE9 Q4QQT3 Q5F3T7 Q5R995
TPG DAA21780

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