BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 11489

Title: RNA aptamer against prion protein in complex with the partial binding peptide   PubMed: 23180780

Deposition date: 2012-03-08 Original release date: 2013-02-11

Authors: Mashima, Tsukasa; Nishikawa, Fumiko; Kamatari, Yuji; Fujiwara, Hiromichi; Nishikawa, Satoshi; Kuwata, Kazuo; Katahira, Masato

Citation: Mashima, Tsukasa; Nishikawa, Fumiko; Kamatari, Yuji; Fujiwara, Hiromichi; Saimura, Masayuki; Nagata, Takashi; Kodaki, Tsutomu; Nishikawa, Satoshi; Kuwata, Kazuo; Katahira, Masato. "Anti-prion activity of an RNA aptamer and its structural basis"  Nucleic Acids Res. 41, 1355-1362 (2013).

Assembly members:
RNA_(5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3'), polymer, 12 residues, 4033.540 Da.
P16, polymer, 12 residues, 1387.577 Da.

Natural source:   Common Name: not available   Taxonomy ID: not available   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
RNA_(5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3'): GGAGGAGGAGGA
P16: GQWNKPSKPKTN

Data sets:
Data typeCount
1H chemical shifts154

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1RNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')_11
2RNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')_21
3entity_2_12
4entity_2_22

Entities:

Entity 1, RNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')_1 12 residues - 4033.540 Da.

1   GGAGGAGGAG
2   GA

Entity 2, entity_2_1 12 residues - 1387.577 Da.

1   GLYGLNTRPASNLYSPROSERLYSPROLYS
2   THRASN

Samples:

sample_1: RNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3') 1 mM; P16 1 mM; potassium phosphate 10 mM; potassium chloride 10 mM; DSS 0.01 mM; sodium azide 3 mM; H2O 95%; D2O 5%

sample_2: RNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3') 1 mM; P16 1 mM; potassium phosphate 10 mM; potassium chloride 10 mM; DSS 0.01 mM; sodium azide 3 mM; D2O 100%

sample_conditions_1: ionic strength: 20 mM; pH: 6.2; pressure: 1 atm; temperature: 278 K

sample_conditions_2: ionic strength: 20 mM; pH: 6.2; pressure: 1 atm; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_2
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_2
2D 1H-1H TOCSYsample_1isotropicsample_conditions_2
2D 1H-1H TOCSYsample_2isotropicsample_conditions_2
2D DQF-COSYsample_1isotropicsample_conditions_2
2D DQF-COSYsample_2isotropicsample_conditions_2
2D 1H-13C HSQCsample_2isotropicsample_conditions_2
JRHMBCsample_1isotropicsample_conditions_2

Software:

X-PLOR NIH v2.26, Schwieters, Kuszewski, Tjandra and Clore - refinement

xwinnmr, Bruker Biospin - collection

TOPSPIN, Bruker Biospin - collection

SPARKY, Goddard - chemical shift assignment, peak picking

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

TALOS, Cornilescu, Delaglio and Bax - data analysis

NMR spectrometers:

  • Bruker DRX 600 MHz