BMRB Entry 19276

Name: Structure of d[CGCGAAGCATTCGCG] hairpin
Published: 2013-07-08

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PDB ID: 2m8y
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR19276
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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:

Structure of d[CGCGAAGCATTCGCG] hairpin

Deposition date:

2013-05-30

Original release date:

2013-07-08

Authors:

Lim, Kah Wai; Phan, Anh Tuan

Citation:

Citation: Lim, Kah Wai; Phan, Anh Tuan. "Structural basis of DNA quadruplex-duplex junction formation." Angew. Chem. Int. Ed. Engl. 52, 8566-8569 (2013).
PubMed: 23794476

Assembly members:

Assembly members:
DNA_(5'-D(*CP*GP*CP*GP*AP*AP*GP*CP*AP*TP*TP*CP*GP*CP*G)-3'), polymer, 15 residues, 4595.023 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):
DNA_(5'-D(*CP*GP*CP*GP*AP*AP*GP*CP*AP*TP*TP*CP*GP*CP*G)-3'): CGCGAAGCATTCGCG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	139

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA (5'-D(CPGPCPGPAPAPGPCPAPTPTPCPGPCP*G)-3')	1

Entities:

Entity 1, DNA (5'-D(*CP*GP*CP*GP*AP*AP*GP*CP*AP*TP*TP*CP*GP*CP*G)-3') 15 residues - 4595.023 Da.

1

DC

DG

DC

DG

DA

DG

DC

DA

DT

2

DT

DC

DG

DC

DG

Samples:

DNA-1: DNA (5'-D(*CP*GP*CP*GP*AP*AP*GP*CP*AP*TP*TP*CP*GP*CP*G)-3') 0.5-2.0 mM; H2O 90%; D2O 10%

DNA-2: DNA (5'-D(*CP*GP*CP*GP*AP*AP*GP*CP*AP*TP*TP*CP*GP*CP*G)-3') 0.5-2.0 mM; D2O 100%

DNA-3: DNA (5'-D(*CP*GP*CP*GP*AP*AP*GP*CP*AP*TP*TP*CP*GP*CP*G)-3'), [U-2% 15N], 0.5-2.0 mM; H2O 90%; D2O 10%

DNA-4: DNA (5'-D(*CP*GP*CP*GP*AP*AP*GP*CP*AP*TP*TP*CP*GP*CP*G)-3'), [U-100% 2H], 0.5-2.0 mM; D2O 100%

sample_conditions_1: ionic strength: 40 mM; pH: 7; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 40 mM; pH: 7; pressure: 1 atm; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	DNA-2	isotropic	sample_conditions_1
2D 1H-1H JR NOESY	DNA-1	isotropic	sample_conditions_2
2D 1H-1H COSY	DNA-2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	DNA-2	isotropic	sample_conditions_1
2D 1H-13C HSQC	DNA-2	isotropic	sample_conditions_1
2D 1H-13C JR HMBC	DNA-1	isotropic	sample_conditions_1
2D 1H-31P HSQC	DNA-2	isotropic	sample_conditions_1
H-D EXCHANGE	DNA-2	isotropic	sample_conditions_1
15N-FILTERED	DNA-3	isotropic	sample_conditions_1
D-LABELED	DNA-4	isotropic	sample_conditions_1

Software:

TOPSPIN v2.1, Bruker Biospin - processing

FELIX v2007, Felix NMR, Inc. - peak picking

X-PLOR NIH v2.29, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

Bruker Avance 400 MHz
Bruker Avance 600 MHz
Bruker Avance 700 MHz