BMRB Entry 30940

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:
Data typeCount
1H chemical shifts177
31P chemical shifts12

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22

Entities:

Entity 1, unit_1 19 residues - 6148.762 Da.

1   AUCCAGAAAC
2   GGAUGGAUA

Entity 2, unit_2 5 residues - 1603.071 Da.

1   OMULCCOMCLCGOMU

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:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-31P COSYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_2
2D 1H-1H TOCSYsample_2isotropicsample_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