BMRB Entry 30868

Name: Solution structure of the HIV-1 PBS-segment
Published: 2021-03-12

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PDB ID: 7lva
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30868
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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 the HIV-1 PBS-segment

Deposition date:

2021-02-24

Original release date:

2021-03-12

Authors:

Heng, X.; Song, Z.

Citation:

Citation: Song, Zhenwei; Gremminger, Thomas; Singh, Gatikrushna; Cheng, Yi; Li, Jun; Qiu, Liming; Ji, Juan; Lange, Margaret; Zuo, Xiaobing; Chen, Shi-Jie; Zou, Xiaoqin; Boris-Lawrie, Kathleen; Heng, Xiao. "The three-way junction structure of the HIV-1 PBS-segment binds host enzyme important for viral infectivity" Nucleic Acids Res. 49, 5925-5942 (2021).
PubMed: 33978756

Assembly members:

Assembly members:
entity_1, polymer, 103 residues, 33249.836 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GGCUCUGGUAACUAGAGAUC CCUCAGACCCUUUUAGUCAG UGUGGAAAAUCUCUAGCAGU GGCGCCCGAACAGGGACUUG AAAGCGAAAGUAAAGCCAGA GCC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	474

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 103 residues - 33249.836 Da.

1

G

C

U

C

U

G

U

A

2

A

C

U

A

G

A

G

A

U

C

3

C

U

C

A

G

A

C

4

U

A

G

U

C

A

G

5

U

G

U

G

A

U

6

C

U

C

U

A

G

C

A

G

U

7

G

C

G

C

G

A

8

C

A

G

A

C

U

G

9

A

G

C

G

A

G

10

U

A

G

C

A

G

A

11

G

C

Samples:

sample_1: RNA (103-MER), 1H, 250 uM

sample_2: RNA (103-MER), [A-8D, C-D, G-H, U-5,6-D2], 250 uM

sample_3: RNA (103-MER), [A-8D, C-D, G-8D, U-H], 250 uM

sample_4: RNA (103-MER), [A-8D, C-5,6-D2, G-D, U-5,6-D2], 250 uM

sample_5: RNA (103-MER), [A-8D, C-D, G-8D, U-D], 250 uM

sample_6: RNA (103-MER), [A-H, C-D, G-H, U-D], 250 uM

sample_7: RNA (103-MER), [A-H, C-H, G-D, U-D], 250 uM

sample_conditions_1: ionic strength: 3 mM; pH: 7.5 pD; pressure: 1 atm; temperature: 308 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_3	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_4	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_5	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_6	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_7	isotropic	sample_conditions_1

Software:

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView, Johnson, One Moon Scientific - chemical shift assignment, peak picking

CYANA, Guntert, Mumenthaler and Wuthrich - geometry optimization, structure calculation

Amber, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman - refinement

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

Bruker AVANCE 800 MHz