BMRB Entry 25571

Name: HIV-1 Core Packaging Signal
Published: 2015-05-26

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PDB ID: 2n1q
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25571
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: HIV-1 Core Packaging Signal PubMed: 25999508

Deposition date: 2015-04-15 Original release date: 2015-05-26

Authors: Keane, Sarah; Summers, Michael

Citation: Keane, Sarah; Heng, Xiao; Lu, Kun; Kharytonchyk, Siarhei; Ramakrishnan, Venkateswaran; Carter, Gregory; Barton, Shawn; Hosic, Azra; Florwick, Alyssa; Santos, Justin; Bolden, Nicholas; McCowin, Sayo; Case, David; Johnson, Bruce; Salemi, Marco; Telesnitsky, Alice; Summers, Michael. "RNA structure. Structure of the HIV-1 RNA packaging signal" Science 348, 917-921 (2015).

Assembly members:
RNA_(155-MER), polymer, 155 residues, 50544.359 Da.

Natural source: Common Name: AIDS virus Taxonomy ID: 12721 Superkingdom: Viruses Kingdom: not available Genus/species: Lentivirus Human immunodeficiency virus

Experimental source: Production method: enzymatic semisynthesis Host organism: HIV

Entity Sequences (FASTA):
RNA_(155-MER): GGUGCCCGUCUGUUGUGUGA CUCUGGUGAGAGCCAGAGGA GAUCUCUCGACGCAGGACUC GGCUUGCUGGAGACGGCAAG AGGCGAGGGGCGGCGACUGG UGAGUACGCCAAAAAUUUUG ACUAGCGGAGGCUAGAAGGA GAGAGAUGGGUGCCC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	695

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (155-MER)	1

Entities:

Entity 1, RNA (155-MER) 155 residues - 50544.359 Da.

1

G

U

G

C

G

U

C

2

U

G

U

G

U

G

U

G

A

3

C

U

C

U

G

U

G

A

G

4

A

G

C

A

G

A

G

A

5

G

A

U

C

U

C

U

C

G

A

6

C

G

C

A

G

A

C

U

C

7

G

C

U

G

C

U

G

8

A

G

A

C

G

C

A

G

9

A

G

C

G

A

G

10

C

G

C

G

A

C

U

G

11

U

G

A

G

U

A

C

G

C

12

A

U

G

13

A

C

U

A

G

C

G

A

G

14

G

C

U

A

G

A

G

A

15

G

A

G

A

G

A

U

G

16

U

G

C

Samples:

ACGU: RNA (155-MER) 300 mM; TRIS, [U-2H], 20 mM; D2O 100%

A: RNA (155-MER), A-H, C-D, G-D, U-D, 300 mM; TRIS, [U-2H], 20 mM; D2O 100%

G: RNA (155-MER), A-D, C-D, G-H, U-D, 300 mM; TRIS, [U-2H], 20 mM; D2O 100%

C: RNA (155-MER), A-D, C-H, G-D, U-D, 300 mM; TRIS, [U-2H], 20 mM; D2O 100%

U6r: RNA (155-MER), A-D, C-D, G-D, U-5D, 300 mM; TRIS, [U-2H], 20 mM; D2O 100%

A2rGr: RNA (155-MER), A-8D, C-D, G-8D, U-D, 300 mM; TRIS, [U-2H], 20 mM; D2O 100%

A2rCr: RNA (155-MER), A-8D, C-5,6-D2, G-D, U-D, 300 mM; TRIS, [U-2H], 20 mM; D2O 100%

A2rUr: RNA (155-MER), A-8D, C-D, G-D, U-5,6-D2, 300 mM; TRIS, [U-2H], 20 mM; D2O 100%

A2rGrCr: RNA (155-MER), A-8D, C-5,6-D2, G-8D, U-D, 300 mM; TRIS, [U-2H], 20 mM; D2O 100%

A2rGrUr: RNA (155-MER), A-8D, C-D, G-8D, U-5,6-D2, 300 mM; TRIS, [U-2H], 20 mM; D2O 100%

A2rCrUr: RNA (155-MER), A-8D, C-5,6-D2, G-D, U-5,6-D2, 300 mM; TRIS, [U-2H], 20 mM; D2O 100%

A2Ur: RNA (155-MER), A-8,1',2',3',4',5',5 -D7, C-D, G-D, U-5,6-D2, 300 mM; TRIS, [U-2H], 20 mM; D2O 100%

A2GrUr: RNA (155-MER), A-8,1',2',3',4',5',5 -D7, C-D, G-8D, U-5,6-D2, 300 mM; TRIS, [U-2H], 20 mM; D2O 100%

AG8: RNA (155-MER), A-H, C-D, G-1',2',3',4',5',5''-D6 , U-D, 300 mM; TRIS, [U-2H], 20 mM; D2O 100%

GA8: RNA (155-MER), A-2,1',2',3',4',5',5-D7, C-D, G-H, U-D, 300 mM; TRIS, [U-2H], 20 mM; D2O 100%

UA8: RNA (155-MER), A-2,1',2',3',4',5',5-D7, C-D, G-D, U-H, 300 mM; TRIS, [U-2H], 20 mM; D2O 100%

GUr: RNA (155-MER), A-D, C-D, G-H, U-5,6-D2, 300 mM; TRIS, [U-2H], 20 mM; D2O 100%

G8Ur: RNA (155-MER), A-D, C-D, G-1',2',3',4',5',5''-D6 , U-5,6-D2, 300 mM; TRIS, [U-2H], 20 mM; D2O 100%

G8U6r: RNA (155-MER), A-D, C-D, G-1',2',3',4',5',5''-D6 , U-5D, 300 mM; TRIS, [U-2H], 20 mM; D2O 100%

G8C6r: RNA (155-MER), A-D, C-5D, G-1',2',3',4',5',5''-D6 , U-D, 300 mM; TRIS, [U-2H], 20 mM; D2O 100%

sample_conditions_1: ionic strength: 20 mM; pD: 7.5 pD; pressure: 1 atm; temperature: 308 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	ACGU	isotropic	sample_conditions_1
2D 1H-1H NOESY	A	isotropic	sample_conditions_1
2D 1H-1H NOESY	G	isotropic	sample_conditions_1
2D 1H-1H NOESY	C	isotropic	sample_conditions_1
2D 1H-1H NOESY	U6r	isotropic	sample_conditions_1
2D 1H-1H NOESY	A2rGr	isotropic	sample_conditions_1
2D 1H-1H NOESY	A2rCr	isotropic	sample_conditions_1
2D 1H-1H NOESY	A2rUr	isotropic	sample_conditions_1
2D 1H-1H NOESY	A2rGrCr	isotropic	sample_conditions_1
2D 1H-1H NOESY	A2rGrUr	isotropic	sample_conditions_1
2D 1H-1H NOESY	A2rCrUr	isotropic	sample_conditions_1
2D 1H-1H NOESY	A2Ur	isotropic	sample_conditions_1
2D 1H-1H NOESY	A2GrUr	isotropic	sample_conditions_1
2D 1H-1H NOESY	AG8	isotropic	sample_conditions_1
2D 1H-1H NOESY	GA8	isotropic	sample_conditions_1
2D 1H-1H NOESY	UA8	isotropic	sample_conditions_1
2D 1H-1H NOESY	GUr	isotropic	sample_conditions_1
2D 1H-1H NOESY	G8Ur	isotropic	sample_conditions_1
2D 1H-1H NOESY	G8U6r	isotropic	sample_conditions_1
2D 1H-1H NOESY	G8C6r	isotropic	sample_conditions_1

Software:

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

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

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

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

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure solution

NMR spectrometers:

Bruker Avance 800 MHz
Bruker Avance 600 MHz