BMRB Entry 25671

Name: 1H Chemical Shift Assignments of the HIV ISS element
Published: 2015-11-30

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PDB ID: 2n4l
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25671
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

1H Chemical Shift Assignments of the HIV ISS element

Deposition date:

2015-06-23

Original release date:

2015-11-30

Authors:

Tolbert, Blanton; Jain, Niyati; Morgan, Christopher; Rife, Brittany; Salemi, Marco

Citation:

Citation: Jain, Niyati; Morgan, Christopher; Rife, Brittany; Salemi, Marco; Tolbert, Blanton. "Solution Structure of the HIV-1 Intron Splicing Silencer and Its Interactions with the UP1 Domain of Heterogeneous Nuclear Ribonucleoprotein (hnRNP) A1" J. Biol. Chem. 291, 2331-2344 (2016).
PubMed: 26607354

Assembly members:

Assembly members:
RNA_(53-MER), polymer, 53 residues, 17006.127 Da.

Natural source:

Natural source: Common Name: HIV Taxonomy ID: 11676 Superkingdom: Viruses Kingdom: not available Genus/species: Lentivirus Human immunodeficiency virus 1

Experimental source:

Experimental source: Production method: In vitro transcription Host organism: T7 dependent In vitro Transcription

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_(53-MER): GGAAUAUUUUUGCUGUACUU UCUAUAGUGAAUAGAGUUAG GCAGGGAUAUUCC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	172

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (53-MER)	1

Entities:

Entity 1, RNA (53-MER) 53 residues - 17006.127 Da.

1

G

A

U

A

U

2

U

G

C

U

G

U

A

C

U

3

U

C

U

A

U

A

G

U

G

A

4

A

U

A

G

A

G

U

A

G

5

G

C

A

G

A

U

A

U

6

U

C

Samples:

ISS_1: ISS (53-MER), [U-2H], 80 – 120 uM; D2O, natural abunance, 100%

ISS_2: ISS (53-MER), [U-2H], 80 – 120 uM; D2O, natural abunance, 100%

ISS_3: ISS (53-MER), [U-100% 13C], 80 – 120 uM; D2O, natural abunance, 100%

ISS_conditions_1: ionic strength: 10 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	ISS_1	isotropic	ISS_conditions_1
2D 1H-1H TOCSY	ISS_2	isotropic	ISS_conditions_1
2D 1H-13C HMQC	ISS_3	isotropic	ISS_conditions_1

Software:

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

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

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution

TOPSPIN, Bruker Biospin - collection

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

NMR spectrometers:

Bruker Avance 900 MHz
Bruker Avance 800 MHz
Bruker Avance 500 MHz