BMRB Entry 11176

Name: Solution Structure of RNA aptamer against AML1 Runt domain
Published: 2015-06-23

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PDB ID: 2rrc
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR11176
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution Structure of RNA aptamer against AML1 Runt domain

Deposition date:

2010-06-23

Original release date:

2015-06-23

Authors:

Nomura, Yusuke; Fujiwara, Kazuya; Chiba, Manabu; Fukunaga, Jun-ichi; Tanaka, Yoichiro; Iibuchi, Hiroaki; Tanaka, Taku; Nakamura, Yoshikazu; Kawai, Gota; Kozu, Tomoko; Sakamoto, Taiichi

Citation:

Citation: Nomura, Yusuke; Fukunaga, Jun-ichi; Tanaka, Yoichiro; Fujiwara, Kazuya; Chiba, Manabu; Iibuchi, Hiroaki; Tanaka, Taku; Nakamura, Yoshikazu; Kawai, Gota; Sakamoto, Taiichi; Kozu, Tomoko. "A novel high affinity RNA motif that mimics DNA in AML1 Runt domain binding" .

Assembly members:

Assembly members:
AML22, polymer, 22 residues, 7032 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: enzymatic semisynthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
AML22: GGACCCACCACGGCGAGGUC CA

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	105

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	AML22	1

Entities:

Entity 1, AML22 22 residues - 7032 Da.

1

G

A

C

A

C

A

2

C

G

C

G

A

G

U

C

3

C

A

Samples:

sample_1: AML22 0.6 mM; sodium phosphate 10 mM; D2O 100%

sample_2: AML22, [U-100% 13C; U-100% 15N], 0.5 mM; sodium phosphate 10 mM; D2O 100%

sample_3: AML22 0.6 mM; sodium phosphate 10 mM; H2O 90%; D2O 10%

sample_4: AML22, [U-100% 13C; U-100% 15N], 0.5 mM; sodium phosphate 10 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 283 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY no.1	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY no.2	sample_3	isotropic	sample_conditions_1
2D 1H-1H NOESY no.1	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY no.2	sample_3	isotropic	sample_conditions_1
2D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
2D HCCH-COSY	sample_2	isotropic	sample_conditions_1
2D HNN-COSY	sample_4	isotropic	sample_conditions_1

Software:

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

NMR spectrometers:

Bruker DRX 500 MHz
Bruker DRX 600 MHz