BMRB Entry 7098

Name: Linear dimer of stemloop SL1 from HIV-1
Published: 2007-02-07

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PDB ID: 2gm0
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR7098
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Linear dimer of stemloop SL1 from HIV-1 PubMed: 16603544

Deposition date: 2006-05-05 Original release date: 2007-02-07

Authors: Ulyanov, N.; Mujeeb, A.; Du, Z.; Tonelli, M.; Parslow, T.; James, T.

Citation: Ulyanov, N.; Mujeeb, A.; Du, Z.; Tonelli, M.; Parslow, T.; James, T.. "NMR structure of the full-length linear dimer of stem-loop-1 RNA in the HIV-1 dimer initiation site" J. Biol. Chem. 281, 16168-16177 (2006).

Assembly members:
RNA (35-MER), polymer, 35 residues, Formula weight is not available

Natural source: Common Name: HIV-1 Taxonomy ID: 11676 Superkingdom: Viruses Kingdom: not available Genus/species: Lentivirus HIV-1

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):
RNA (35-MER): GACGGCUUGCUGAAGCGCGC ACGGCAAGAGGCGUC

Data sets:

assigned_chemical_shifts
- chemical_shift_set_1

Data type	Count
13C chemical shifts	137
15N chemical shifts	11
1H chemical shifts	181

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (35-MER), chain A	1
2	RNA (35-MER), chain B	1

Entities:

Entity 1, RNA (35-MER), chain A 35 residues - Formula weight is not available

1

G

A

C

G

C

U

G

C

2

U

G

A

G

C

G

C

G

C

3

A

C

G

C

A

G

A

G

4

G

C

G

U

C

Samples:

sample_1: RNA (35-MER) 0.75 mM; potassium phosphate buffer 10 mM; NaCl 250 mM; MgCl2 0.1 mM; D2O 100%

sample_2: RNA (35-MER) 0.75 mM; potassium phosphate buffer 10 mM; NaCl 250 mM; MgCl2 0.1 mM; H2O 90%; D2O 10%

sample_3: RNA (35-MER), [U-13C; U-15N], 0.75 mM; potassium phosphate buffer 10 mM; NaCl 250 mM; MgCl2 0.1 mM; D2O 100%

sample_4: RNA (35-MER), [U-13C; U-15N], 0.75 mM; potassium phosphate buffer 10 mM; NaCl 250 mM; MgCl2 0.1 mM; H2O 90%; D2O 10%

sample_cond_1: ionic strength: 260 mM; pH: 6.4; pressure: 1 atm; temperature: 303 K

sample_cond_2: ionic strength: 260 mM; pH: 6.4; pressure: 1 atm; temperature: 288 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NOESY	not available	not available	not available
2D TOCSY	not available	not available	not available
3D 13C-separated NOESY	not available	not available	not available
non-decoupled constant-time 1H-13C TROSY-HSQC	not available	not available	not available
2D 1H-15N HSQC	not available	not available	not available

Software:

VNMR v6.1 - collection

NMRPipe v2.3 - processing

MARDIGRAS v3.21 - iterative matrix relaxation

SPARKY v3.110 - data analysis

DYANA v1.5 - refinement

miniCarlo - refinement

NMR spectrometers:

Varian Unity Inova 900 MHz