BMRB Entry 6077

Title:
Loop B RNAs from the Stem-Loop IV domain of the Enterovirus Internal Ribosome Entry Site with a Six-nucleotide Bulge AUUCCU   PubMed: 15134450
Deposition date:
2004-01-13
Original release date:
2004-06-30
Authors:
Du, Z.; Ulyanov, N.; Yu, J.; James, T.
Citation:

Citation: Du, Z.; Ulyanov, N.; Yu, J.; Andino, R.; James, T.. "NMR Structures of Loop B RNAs from the Stem-Loop IV Domain of the Enterovirus Internal Ribosome Entry Site: A Single C-to-U Substitution Drastically Changes the Shape and Flexibility of RNA"  Biochemistry 43, 5757-5771 (2004).

Assembly members:

Assembly members:

Natural source:

Natural source:   Common Name: Enterovirus poliovirus   Taxonomy ID: 138953   Superkingdom: Viruses   Kingdom: not available   Genus/species: Enterovirus poliovirus

Experimental source:   Production method: enzymatic semisynthesis

Experimental source:

Natural source:   Common Name: Enterovirus poliovirus   Taxonomy ID: 138953   Superkingdom: Viruses   Kingdom: not available   Genus/species: Enterovirus poliovirus

Experimental source:   Production method: enzymatic semisynthesis

Entity Sequences (FASTA):

Data sets:
Data typeCount
13C chemical shifts89
1H chemical shifts407

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID

Entities:

Samples:

sample_1: RNA FRAGMENT OF DOMAIN IV STEM-LOOP B OF ENTEROVIRAL IRES1.0 – 2.0 mM; NaCl 25 mM; sodium phosphate buffer 25 mM; H2O 90%; D2O 10%

sample_2: RNA FRAGMENT OF DOMAIN IV STEM-LOOP B OF ENTEROVIRAL IRES1.0 – 2.0 mM; NaCl 25 mM; sodium phosphate buffer 25 mM; D2O 100%

sample_3: RNA FRAGMENT OF DOMAIN IV STEM-LOOP B OF ENTEROVIRAL IRES, [U-13C; U-15N]-A, U, 1.0 – 2.0 mM; NaCl 25 mM; sodium phosphate buffer 25 mM; D2O 100%

sample_4: RNA FRAGMENT OF DOMAIN IV STEM-LOOP B OF ENTEROVIRAL IRES, [U-13C; U-15N]-A, U, 1.0 – 2.0 mM; NaCl 25 mM; sodium phosphate buffer 25 mM; D2O 100%; C12E6/N-HEXANOL MIXTURE (MOLAR RATIO 0.64) 5%

sample_cond_1: ionic strength: 50 mM; pH*: 6.5; pressure: 1 atm; temperature: 298 K

sample_cond_2: ionic strength: 50 mM; pH*: 6.5; pressure: 1 atm; temperature: 278 K

Experiments:

NameSampleSample stateSample conditions
2D NOESYnot availablenot availablenot available
DQF-COSYnot availablenot availablenot available
1H-13C CONSTANT TIME HSQCnot availablenot availablenot available

Software:

VNMR v6.1 - collection

NMRPipe v2.1 - processing

MARDIGRAS v3.2 - iterative matrix relaxation

DYANA v1.5 - refinement

AMBER v7 - refinement

NMR spectrometers:

  • Varian INOVA 600 MHz