BMRB Entry 17083

Name: Structure of a conserved retroviral RNA packaging element by NMR spectroscopy and cryo-electron tomography
Published: 2010-10-14

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PDB ID: 2l1f
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17083
MolProbity Validation Chart

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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:

Structure of a conserved retroviral RNA packaging element by NMR spectroscopy and cryo-electron tomography

Deposition date:

2010-07-28

Original release date:

2010-10-14

Authors:

Summers, Michael; Irobalieva, Rossitza; Tolbert, Blanton; Smalls-Manty, Adjoa; Iyalla, Kilali; Loeliger, Kelsey; D'Souza, Victoria; Khant, Htet; Schmid, Michael; Garcia, Eric; Telesnitsky, Alice; Chiu, Wah; Miyazaki, Yasuyuki

Citation:

Citation: Miyazaki, Yasuyuki; Irobalieva, Rossitza; Tolbert, Blanton; Smalls-Mantey, Adjoa; Iyalla, Kilali; Loeliger, Kelsey; Khant, Victoria; Schmid, Htet; Garcia, Michael; Telesnitsky, Eric; Chiu, Alice; Summers, Wah. "Structure of a conserved retroviral RNA packaging element by NMR spectroscopy and cryo-electron tomography." J. Mol. Biol. 404, 751-772 (2010).
PubMed: 20933521

Assembly members:

Assembly members:
RNA_(65-MER), polymer, 65 residues, 21071.766 Da.
RNA_(66-MER), polymer, 66 residues, 21416.973 Da.

Natural source:

Natural source: Common Name: Moloney Murine Leukemia Virus Taxonomy ID: 11801 Superkingdom: Virus Kingdom: not available Genus/species: Gammaretrovirus not available

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Moloney Murine Leukemia Virus Vector: pMoMuLV-SL-CD-HDV

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_(65-MER): GGCGGACCCGUGGUGGAACA GACGUGUUCGGAACACCCGG CCGCAACCCUGGGAGACGUC CCAGG
RNA_(66-MER): GGCGGACCCGUGGUGGAACA GACGUGUUCGGAACACCCGG CCGCAACCCUGGGAGACGUC CCAGGG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	208

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (65-MER)	1
2	RNA (66-MER)	2

Entities:

Entity 1, RNA (65-MER) 65 residues - 21071.766 Da.

1

G

C

G

A

C

G

2

U

G

U

G

A

C

A

3

G

A

C

G

U

G

U

C

G

4

G

A

C

A

C

G

5

C

G

C

A

C

U

6

G

A

G

A

C

G

U

C

7

C

A

G

Entity 2, RNA (66-MER) 66 residues - 21416.973 Da.

1

G

C

G

A

C

G

2

U

G

U

G

A

C

A

3

G

A

C

G

U

G

U

C

G

4

G

A

C

A

C

G

5

C

G

C

A

C

U

6

G

A

G

A

C

G

U

C

7

C

A

G

Samples:

sample_1: RNA (65-MER), [U-2H], 400 – 800 uM; D2O 100 ± 100 %

sample_conditions_1: ionic strength: 80 mM; pH: 7.0; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NOESY	sample_1	isotropic	sample_conditions_1
2D NOESY	sample_1	isotropic	sample_conditions_1

Software:

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

NMR spectrometers:

Bruker DRX 800 MHz
Bruker DRX 600 MHz