BMRB Entry 17972

Name: U2/U6 Helix I
Published: 2012-02-20

Click here to enlarge.

PDB ID: 2lk3
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17972
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
NMR-STAR v2.1 text file (deprecated)
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title: U2/U6 Helix I PubMed: 22328579

Deposition date: 2011-10-03 Original release date: 2012-02-20

Authors: Burke, Jordan; Sashital, Dipali; Zuo, Xiaobing; Wang, Yun-Xing; Butcher, Samuel

Citation: Burke, Jordan; Sashital, Dipali; Zuo, Xiaobing; Wang, Yun-Xing; Butcher, Samuel. "Structure of the yeast U2/U6 snRNA complex." RNA 18, 673-683 (2012).

Assembly members:
RNA_(5'-R(*GP*GP*CP*UP*UP*AP*GP*AP*UP*CP*AP*GP*AP*AP*AP*UP*GP*AP*UP*CP*AP*GP*CP*C)-3')_, polymer, 24 residues, 7716.717 Da.

Natural source: Common Name: baker Taxonomy ID: 4932 Superkingdom: not available Kingdom: not available Genus/species: Eukaryota Fungi

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

Entity Sequences (FASTA):
RNA_(5'-R(*GP*GP*CP*UP*UP*AP*GP*AP*UP*CP*AP*GP*AP*AP*AP*UP*GP*AP*UP*CP*AP*GP*CP*C)-3')_: GGCUUAGAUCAGAAAUGAUC AGCC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
- assigned_chem_shift_2ist_1

Data type	Count
13C chemical shifts	80
1H chemical shifts	167

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	U2_U6snRNA	1

Entities:

Entity 1, U2_U6snRNA 24 residues - 7716.717 Da.

1

G

C

U

A

G

A

U

C

2

A

G

A

U

G

A

U

C

3

A

G

C

Samples:

sample_1: RNA0.5 – 0.6 mM; H2O 90%; D2O 10%

sample_2: RNA0.5 – 0.6 mM; D2O 100%

sample_3: RNA, [U-98% 13C; U-98% 15N], 0.3 mM; H2O 90%; D2O 10%

sample_4: RNA, [U-98% 13C; U-98% 15N], 0.3 mM; D2O 100%

sample_5: RNA, [U-98% 13C; U-98% 15N], 0.3 mM; Pf1 phage 17 mg/ml; H2O 90%; D2O 10%

sample_6: RNA, [U-98% 13C; U-98% 15N], 0.3 mM; Pf1 phage 17 mg/ml; D2O 100%

sample_7: RNA0.5 – 0.6 mM; Pf1 phage 18 mg/ml; D2O 100%

sample_conditions_1: ionic strength: 15 mM; pH: 7.0; pressure: 1 atm; temperature: 283 K

sample_conditions_2: ionic strength: 15 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_2
2D 1H-13C HSQC aromatic	sample_2	isotropic	sample_conditions_2
2D 1H-13C HSQC aliphatic	sample_2	isotropic	sample_conditions_2
2D 1H-15N HMQC	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_4	isotropic	sample_conditions_2
2D 1H-13C HSQC aliphatic	sample_4	isotropic	sample_conditions_2
2D 1H-15N HMQC	sample_5	anisotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_6	anisotropic	sample_conditions_2
2D 1H-13C HSQC aliphatic	sample_6	anisotropic	sample_conditions_2
2D HNN-COSY	sample_3	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_4	isotropic	sample_conditions_2
3D HCCH-COSY	sample_4	isotropic	sample_conditions_2

Software:

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

xwinnmr v3.5, Bruker Biospin - collection, processing

VNMRJ v1.1, Varian - collection

NMRPipe v97.027.12.56, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY v3.114, Goddard - chemical shift assignment, data analysis, peak picking

X-PLOR NIH v2.21, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

Bruker DMX 750 MHz
Varian INOVA 600 MHz