BMRB Entry 11489

Name: RNA aptamer against prion protein in complex with the partial binding peptide
Published: 2013-02-11

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PDB ID: 2ru7
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR11489
MolProbity Validation Chart

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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

RNA aptamer against prion protein in complex with the partial binding peptide

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:

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).
PubMed: 23180780

Assembly members:

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:

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

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	154

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (5'-R(GPGPAPGPGPAPGPGPAPGPGPA)-3')_1	1
2	RNA (5'-R(GPGPAPGPGPAPGPGPAPGPGPA)-3')_2	1
3	entity_2_1	2
4	entity_2_2	2

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

G

A

G

A

G

A

G

2

G

A

Entity 2, entity_2_1 12 residues - 1387.577 Da.

1

GLY

GLN

TRP

ASN

LYS

PRO

SER

LYS

PRO

LYS

2

THR

ASN

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:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_2
2D DQF-COSY	sample_1	isotropic	sample_conditions_2
2D DQF-COSY	sample_2	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_2
JRHMBC	sample_1	isotropic	sample_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