BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 4781

Title: NMR Structure of Stem-loop SL2 of the HIV-1 Psi RNA Packaging Signal Reveals a Novel A-U-A Base-triple Platform   PubMed: 10860728

Authors: Amarasinghe, Gaya; De Guzman, Roberto; Turner, Ryan; Summers, Michael

Citation: Amarasinghe, Gaya; De Guzman, Roberto; Turner, Ryan; Summers, Michael. "NMR Structure of Stem-loop SL2 of the HIV-1 Psi RNA Packaging Signal Reveals a Novel A-U-A Base-triple Platform"  J. Mol. Biol. 299, 145-156 (2000).

Assembly members:
HIV-1 SL2 stem loop, polymer, 19 residues, 6371 Da.
NCp7 protein, polymer, 55 residues, 6372 Da.

Natural source:   Common Name: HIV-1   Taxonomy ID: not available   Superkingdom: Viruses   Kingdom: not available   Genus/species: Lentivirus Human Immunodeficiency virus

Experimental source:   Production method: enzymatic semisynthesis

Entity Sequences (FASTA):
HIV-1 SL2 stem loop: GGCGACUGGUGAGUACGCC
NCp7 protein: MQKGNFRNQRKTVKCFNCGK EGHIAKNCRAPRKKGCWKCG KEGHQMKDCTERQAN

Data sets:
Data typeCount
13C chemical shifts272
15N chemical shifts58
1H chemical shifts456

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1SL2 RNA1
2NCp72

Entities:

Entity 1, SL2 RNA 19 residues - 6371 Da.

1   GGCGACUGGU
2   GAGUACGCC

Entity 2, NCp7 55 residues - 6372 Da.

1   METGLNLYSGLYASNPHEARGASNGLNARG
2   LYSTHRVALLYSCYSPHEASNCYSGLYLYS
3   GLUGLYHISILEALALYSASNCYSARGALA
4   PROARGLYSLYSGLYCYSTRPLYSCYSGLY
5   LYSGLUGLYHISGLNMETLYSASPCYSTHR
6   GLUARGGLNALAASN

Samples:

sample_1: HIV-1 SL2 stem loop0.6 – 1.2 mM; NCp7 protein0.6 – 1.2 mM

sample_2: HIV-1 SL2 stem loop, [U-13C], 0.8 mM; NCp7 protein, [U-13C; U-15N], 0.8 mM

sample_3: HIV-1 SL2 stem loop0.8 – 1.2 mM; NCp7 protein, [U-15N], 0.8 – 1.2 mM

Ex-cond-1: pH*: 6.5; temperature: 298 K

Ex-cond-2: pH*: 6.5; temperature: 278 K

Experiments:

NameSampleSample stateSample conditions
2D NOESYnot availablenot availablenot available
2D TOCSYnot availablenot availablenot available
2D DQF COSYnot availablenot availablenot available
1H-13C HMQCnot availablenot availablenot available
1H,1H,13C HMQC-NOESYnot availablenot availablenot available
1H,1H,13C HCCH-COSYnot availablenot availablenot available
1H,1H,13C HCCH-TOCSYnot availablenot availablenot available
1H,1H,15N HSQC-NOESYnot availablenot availablenot available

Software:

XWINNMR v2.6 - Data aquisition on from the NMR

NMRPipe v1.0 - Data processing

NMRView v3.0 - Data analysis

DYANA v1.5 - Structure calculation

CNS v1.0 - Structure refinement and energy minimization

NMR spectrometers:

  • Bruker Avance DMX 600 MHz
  • Bruker Avance DRX 800 MHz

Related Database Links:

DBJ BAC02557 BAC77486 BAC77487 BAC77511 BAC77512
EMBL CAD26937 CAD26939 CAD26945 CAD26946 CAD26947
GenBank AAA44987 AAA81036 AAB60571 AAC28445 AAD03199
SWISS-PROT P12493 P12497 P35962 P35963 Q73367