BMRB Entry 30940

Name: Hairpin near 3&#039;-Splice Site of Influenza A Segment 7 Bound to 5-nt Oligonucleotide
Published: 2022-01-14

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PDB ID: 7rq5
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30940
MolProbity Validation Chart

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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:

Hairpin near 3'-Splice Site of Influenza A Segment 7 Bound to 5-nt Oligonucleotide

Deposition date:

2021-08-05

Original release date:

2022-01-14

Authors:

Kauffmann, A.; Kennedy, S.; Turner, D.

Citation:

Citation: Kauffmann, A.; Kennedy, S.; Moss, W.; Kierzek, E.; Kierzek, R.; Turner, D.. "Nuclear Magnetic Resonance reveals a two hairpin equilibrium near the 3'-splice site of Influenza A segment 7 mRNA that can be shifted by oligonucleotides" RNA 28, 508-522 (2022).
PubMed: 34983822

Assembly members:

Assembly members:
entity_1, polymer, 19 residues, 6148.762 Da.
entity_2, polymer, 5 residues, 1603.071 Da.

Natural source:

Natural source: Common Name: Influenza A virus Taxonomy ID: 11320 Superkingdom: Viruses Kingdom: not available Genus/species: Alphainfluenzavirus Influenza A virus

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: AUCCAGAAACGGAUGGAUA
entity_2: XXXXX

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	177
31P chemical shifts	12

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	2

Entities:

Entity 1, unit_1 19 residues - 6148.762 Da.

1

A

U

C

A

G

A

C

2

G

A

U

G

A

U

A

Entity 2, unit_2 5 residues - 1603.071 Da.

1

OMU

LCC

OMC

LCG

OMU

Samples:

sample_1: RNA (5'-R(*AP*UP*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*AP*UP*A)-3') 0.5 ± .02 mM; RNA (5'-D(*(MU5)P*(MLC)P*(MRC))-R(P*(LG)P*(MU3))-3') 0.49 ± .02 mM; potassium phosphate 10 ± 0.5 mM; sodium EDTA 0.05 ± .01 mM

sample_2: RNA (5'-R(*AP*UP*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*AP*UP*A)-3') 0.5 ± .02 mM; RNA (5'-D(*(MU5)P*(MLC)P*(MRC))-R(P*(LG)P*(MU3))-3') 0.49 ± .02 mM; potassium phosphate 10 ± 0.5 mM; sodium EDTA 0.05 ± .01 mM

sample_conditions_1: ionic strength: 11 mM; pH: 6.2; pressure: 1 atm; temperature: 293 K

sample_conditions_2: ionic strength: 11 mM; pH: 6.2; pressure: 1 atm; temperature: 274 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-31P COSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	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

Software:

NMRFAM-SPARKY, Lee - chemical shift assignment, data analysis

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

VNMR, Varian - collection

Amber, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman - structure calculation

NMR spectrometers:

Varian UNITY 600 MHz