BMRB Entry 15915

Title:
NMR structure of the human tRNALys3 bound to the HIV genome Loop I
Deposition date:
2008-08-09
Original release date:
2008-09-30
Authors:
Bilbille, Yann; Vendeix, Franck; Guenther, Richard; Malkiewicz, Andrzej; Ariza, Xavier; Vilarrasa, Jaume; Agris, Paul
Citation:

Citation: Bilbille, Yann; Vendeix, Franck; Guenther, Richard; Malkiewicz, Andrzej; Ariza, Xavier; Vilarrasa, Jaume; Agris, Paul. "The structure of the human tRNALys3 anticodon bound to the HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs"  Nucleic Acids Res. 37, 3342-3353 (2009).
PubMed: 19324888

Assembly members:

Assembly members:
RNA_(5'-R(*GP*CP*GP*GP*UP*GP*UP*AP*AP*AP*AP*G)-3'), polymer, 12 residues, 3915.436 Da.
T-RNA_(5'-R(*CP*UP*(2SU)P*UP*UP*AP*AP*(PSU)P*CP*UP*GP*C)-3'), polymer, 12 residues, 3386.044 Da.

Natural source:

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_(5'-R(*GP*CP*GP*GP*UP*GP*UP*AP*AP*AP*AP*G)-3'): GCGGUGUAAAAG
T-RNA_(5'-R(*CP*UP*(2SU)P*UP*UP*AP*AP*(PSU)P*CP*UP*GP*C)-3'): CUXUUAAXCUGC

Data typeCount
1H chemical shifts252

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1RNA (5'-R(*GP*CP*GP*GP*UP*GP*UP*AP*AP*AP*AP*G)-3')1
2T-RNA (5'-R(*CP*UP*(2SU)P*UP*UP*AP*AP*(PSU)P*CP*UP*GP*C)-3')2

Entities:

Entity 1, RNA (5'-R(*GP*CP*GP*GP*UP*GP*UP*AP*AP*AP*AP*G)-3') 12 residues - 3915.436 Da.

1   GCGGUGUAAA
2   AG

Entity 2, T-RNA (5'-R(*CP*UP*(2SU)P*UP*UP*AP*AP*(PSU)P*CP*UP*GP*C)-3') 12 residues - 3386.044 Da.

1   CU2SUUUAAPSUCU
2   GC

Samples:

vgps-H2O_D2O: RNA (5'-R(*GP*CP*GP*GP*UP*GP*UP*AP*AP*AP*AP*G)-3') 0.3-1.2 mM; T-RNA (5'-R(*CP*UP*(2SU)P*UP*UP*AP*AP*(PSU)P*CP*UP*GP*C)-3') 0.3-1.2 mM; sodium phosphate 10 mM; sodium chloride 100 mM; H2O 90%; D2O, [U-100% 2H], 10%

vgps-D2O: RNA (5'-R(*GP*CP*GP*GP*UP*GP*UP*AP*AP*AP*AP*G)-3') 0.3-1.2 mM; T-RNA (5'-R(*CP*UP*(2SU)P*UP*UP*AP*AP*(PSU)P*CP*UP*GP*C)-3') 0.3-1.2 mM; sodium phosphate 10 mM; sodium chloride 100 mM; D2O, [U-100% 2H], 100%

sample_conditions_276: ionic strength: 100 mM; pH: 6.5; pressure: 1 atm; temperature: 276 K

sample_conditions_293: ionic strength: 100 mM; pH: 6.5; pressure: 1 atm; temperature: 293 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYvgps-H2O_D2Oisotropicsample_conditions_276
2D 1H-1H NOESYvgps-H2O_D2Oisotropicsample_conditions_293
2D 1H-13C HSQCvgps-D2Oisotropicsample_conditions_293
2D DQF-COSYvgps-D2Oisotropicsample_conditions_293
2D 1H-1H NOESYvgps-D2Oisotropicsample_conditions_293
2D 1H-15N HSQCvgps-H2O_D2Oisotropicsample_conditions_276

Software:

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

SPARKY, Goddard - chemical shift assignment

Molmol, Koradi, Billeter and Wuthrich - data analysis

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

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

NMRView, Johnson, One Moon Scientific - data analysis

xwinnmr, Bruker Biospin - collection

NMR spectrometers:

  • Bruker Avance 500 MHz
  • Varian INOVA 600 MHz