BMRB Entry 36393

Name: Solution structure of an RNA derived from the joint region of the TAR and PolyA stems of HIV-1 genomic RNA
Published: 2025-10-13

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PDB ID: 7dd4
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36393
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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:

Solution structure of an RNA derived from the joint region of the TAR and PolyA stems of HIV-1 genomic RNA

Deposition date:

2020-10-27

Original release date:

2025-10-13

Authors:

Obayashi, C.; Shinohara, Y.; Masuda, T.; Kawai, G.

Citation:

Citation: Obayashi, C.; Shinohara, Y.; Masuda, T.; Kawai, G.. "Influence of the 5'-terminal sequences on the 5'-UTR structure of HIV-1 genomic RNA." Sci. Rep. 11, 10920-10920 (2021).
PubMed: 34035384

Assembly members:

Assembly members:
RNA (36-MER), polymer, 36 residues, 11558.872 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 11676 Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: chemical synthesis Host organism: unidentified

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA (36-MER): GGUCUCUCUUCGGGGAACCC ACUGCGAAAGUAGUGU

Data sets:

assigned_chemical_shifts
- test_table1.txt

Data type	Count
1H chemical shifts	162

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 36 residues - 11558.872 Da.

1

G

U

C

U

C

U

C

U

2

C

G

A

C

3

A

C

U

G

C

G

A

G

4

U

A

G

U

G

U

Samples:

sample_1: RNA (36-MER), [U-10% 13C; U-15N], 100 uM; sodium chloride 50 mM; sodium phosphate 20 mM; H2O 95%; D2O, [U-2H], 5%

sample_conditions_1: ionic strength: 50 mM; pH: 6.5; pressure: 1 atm; temperature: 283 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NOESY	sample_1	isotropic	sample_conditions_1
2D HOHAHA	sample_1	isotropic	sample_conditions_1
2D NOESY	sample_1	isotropic	sample_conditions_1
2D HOHAHA	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1

Software:

CNS v1.3, Brunger, Adams, Clore, Gros, Nilges and Read - structure calculation

Sparky, Goddard - chemical shift assignment

Sparky, Goddard - peak picking

NMR spectrometers:

Bruker AVANCE 600 MHz
Bruker AVANCE 800 MHz