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Found 1 Document (1.653 seconds)

BMRB: 4781

1F6U

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

Authors

Amarasinghe, G.K., De Guzman, R.N., Turner, R.B., Summers, M.F.

Assembly

SL2 stem loop RNA from HIV-1

Entity

1. HIV-1 SL2 stem loop (polymer, Thiol state: not present), 19 monomers, 6211.684 Da Detail

GGCGACUGGU GAGUACGCC

2. NCp7 protein (polymer, Thiol state: not reported), 55 monomers, 6369.356 Da Detail

MQKGNFRNQR KTVKCFNCGK EGHIAKNCRA PRKKGCWKCG KEGHQMKDCT ERQAN

Total weight

12581.04 Da

Max. entity weight

6369.356 Da

Source organism

Human immunodeficiency virus

Exptl. method

NMR

Refine. method

distance geometry, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 71.6 %, Completeness: 59.9 %, Completeness (bb): 51.2 % Detail

Polymer type: polyribonucleotide polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	59.9 % (577 of 964)	62.9 % (331 of 526)	51.5 % (187 of 363)	78.7 % (59 of 75)
Backbone	51.2 % (275 of 537)	48.5 % (111 of 229)	44.5 % (113 of 254)	94.4 % (51 of 54)
Sidechain	73.3 % (349 of 476)	74.1 % (220 of 297)	76.6 % (121 of 158)	38.1 % (8 of 21)
Aromatic	31.1 % (38 of 122)	29.5 % (18 of 61)	38.8 % (19 of 49)	8.3 % (1 of 12)
Methyl	100.0 % (18 of 18)	100.0 % (9 of 9)	100.0 % (9 of 9)

1. HIV-1 SL2 stem loop

GGCGACUGGU GAGUACGCC

2. NCp7 protein

MQKGNFRNQR KTVKCFNCGK EGHIAKNCRA PRKKGCWKCG KEGHQMKDCT ERQAN

Show sample condition

Sample #1

Temperature 298 (±2) K, Details natural abundance

#	Name	Isotope labeling	Type	Concentration
1	HIV-1 SL2 stem loop			0.6 ~ 1.2 mM
2	NCp7 protein			0.6 ~ 1.2 mM

Sample #2

Temperature 298 (±2) K

#	Name	Isotope labeling	Type	Concentration
3	HIV-1 SL2 stem loop	[U-13C]		0.8 mM
4	NCp7 protein	[U-13C; U-15N]		0.8 mM

Sample #3

Temperature 298 (±2) K

#	Name	Isotope labeling	Type	Concentration
5	HIV-1 SL2 stem loop			0.8 ~ 1.2 mM
6	NCp7 protein	[U-15N]		0.8 ~ 1.2 mM

Chem. Shift Complete2

Sequence coverage: 32.4 %, Completeness: 42.2 %, Completeness (bb): 41.3 % Detail

Polymer type: polyribonucleotide polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	42.2 % (813 of 1928)	42.8 % (450 of 1052)	41.2 % (299 of 726)	42.7 % (64 of 150)
Backbone	41.3 % (444 of 1074)	42.4 % (194 of 458)	38.2 % (194 of 508)	51.9 % (56 of 108)
Sidechain	44.1 % (420 of 952)	43.1 % (256 of 594)	49.4 % (156 of 316)	19.0 % (8 of 42)
Aromatic	41.0 % (100 of 244)	40.2 % (49 of 122)	51.0 % (50 of 98)	4.2 % (1 of 24)
Methyl	50.0 % (18 of 36)	50.0 % (9 of 18)	50.0 % (9 of 18)

1. HIV-1 SL2 stem loop

GGCGACUGGU GAGUACGCC

2. NCp7 protein

MQKGNFRNQR KTVKCFNCGK EGHIAKNCRA PRKKGCWKCG KEGHQMKDCT ERQAN

Show sample condition

Sample #1

Temperature 298 (±2) K, Details natural abundance

#	Name	Isotope labeling	Type	Concentration
1	HIV-1 SL2 stem loop			0.6 ~ 1.2 mM
2	NCp7 protein			0.6 ~ 1.2 mM

Sample #2

Temperature 298 (±2) K

#	Name	Isotope labeling	Type	Concentration
3	HIV-1 SL2 stem loop	[U-13C]		0.8 mM
4	NCp7 protein	[U-13C; U-15N]		0.8 mM

Sample #3

Temperature 298 (±2) K

#	Name	Isotope labeling	Type	Concentration
5	HIV-1 SL2 stem loop			0.8 ~ 1.2 mM
6	NCp7 protein	[U-15N]		0.8 ~ 1.2 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 1F6U, Strand ID: A Detail

Release date

2000-07-09

Citation

NMR structure of stem-loop SL2 of the HIV-1 psi RNA packaging signal reveals a novel A-U-A base-triple platform
Amarasinghe, G.K., De Guzman, R.N., Turner, R.B., Summers, M.F.
J. Mol. Biol. (2000), 299, 145-156, PubMed 10860728 , DOI 10.1006/jmbi.2000.3710 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 4780 released on 2002-04-03
Title NMR Structure of Stem-loop SL2 of the HIV-1 Psi RNA Packaging Signal Reveals a Novel A-U-A Base-triple Platform

Related entities 1. HIV-1 SL2 stem loop, : 1 : 1 entities Detail

Related entities 2. NCp7 protein, : 1 : 2 : 12 : 160 entities Detail

Interaction partners 2. NCp7 protein, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 8 experiments Detail

1 2D NOESY

Instrument

#1 Model Bruker Avance DMX (600 MHz)

#2 Model Bruker Avance DRX (800 MHz)

Sample #1

Details natural abundance

#	Name	Isotope labeling	Type	Concentration
1	HIV-1 SL2 stem loop			0.6 ~ 1.2 mM
2	NCp7 protein			0.6 ~ 1.2 mM

Sample #2

#	Name	Isotope labeling	Type	Concentration
3	HIV-1 SL2 stem loop	[U-13C]		0.8 mM
4	NCp7 protein	[U-13C; U-15N]		0.8 mM

Sample #3

#	Name	Isotope labeling	Type	Concentration
5	HIV-1 SL2 stem loop			0.8 ~ 1.2 mM
6	NCp7 protein	[U-15N]		0.8 ~ 1.2 mM

2 2D TOCSY

Instrument

#1 Model Bruker Avance DMX (600 MHz)

#2 Model Bruker Avance DRX (800 MHz)

Sample #1

Details natural abundance

#	Name	Isotope labeling	Type	Concentration
1	HIV-1 SL2 stem loop			0.6 ~ 1.2 mM
2	NCp7 protein			0.6 ~ 1.2 mM

Sample #2

#	Name	Isotope labeling	Type	Concentration
3	HIV-1 SL2 stem loop	[U-13C]		0.8 mM
4	NCp7 protein	[U-13C; U-15N]		0.8 mM

Sample #3

#	Name	Isotope labeling	Type	Concentration
5	HIV-1 SL2 stem loop			0.8 ~ 1.2 mM
6	NCp7 protein	[U-15N]		0.8 ~ 1.2 mM

3 2D DQF COSY

Instrument

#1 Model Bruker Avance DMX (600 MHz)

#2 Model Bruker Avance DRX (800 MHz)

Sample #1

Details natural abundance

#	Name	Isotope labeling	Type	Concentration
1	HIV-1 SL2 stem loop			0.6 ~ 1.2 mM
2	NCp7 protein			0.6 ~ 1.2 mM

Sample #2

#	Name	Isotope labeling	Type	Concentration
3	HIV-1 SL2 stem loop	[U-13C]		0.8 mM
4	NCp7 protein	[U-13C; U-15N]		0.8 mM

Sample #3

#	Name	Isotope labeling	Type	Concentration
5	HIV-1 SL2 stem loop			0.8 ~ 1.2 mM
6	NCp7 protein	[U-15N]		0.8 ~ 1.2 mM

4 1H-13C HMQC

Instrument

#1 Model Bruker Avance DMX (600 MHz)

#2 Model Bruker Avance DRX (800 MHz)

Sample #1

Details natural abundance

#	Name	Isotope labeling	Type	Concentration
1	HIV-1 SL2 stem loop			0.6 ~ 1.2 mM
2	NCp7 protein			0.6 ~ 1.2 mM

Sample #2

#	Name	Isotope labeling	Type	Concentration
3	HIV-1 SL2 stem loop	[U-13C]		0.8 mM
4	NCp7 protein	[U-13C; U-15N]		0.8 mM

Sample #3

#	Name	Isotope labeling	Type	Concentration
5	HIV-1 SL2 stem loop			0.8 ~ 1.2 mM
6	NCp7 protein	[U-15N]		0.8 ~ 1.2 mM

5 1H,1H,13C HMQC-NOESY

Instrument

#1 Model Bruker Avance DMX (600 MHz)

#2 Model Bruker Avance DRX (800 MHz)

Sample #1

Details natural abundance

#	Name	Isotope labeling	Type	Concentration
1	HIV-1 SL2 stem loop			0.6 ~ 1.2 mM
2	NCp7 protein			0.6 ~ 1.2 mM

Sample #2

#	Name	Isotope labeling	Type	Concentration
3	HIV-1 SL2 stem loop	[U-13C]		0.8 mM
4	NCp7 protein	[U-13C; U-15N]		0.8 mM

Sample #3

#	Name	Isotope labeling	Type	Concentration
5	HIV-1 SL2 stem loop			0.8 ~ 1.2 mM
6	NCp7 protein	[U-15N]		0.8 ~ 1.2 mM

6 1H,1H,13C HCCH-COSY

Instrument

#1 Model Bruker Avance DMX (600 MHz)

#2 Model Bruker Avance DRX (800 MHz)

Sample #1

Details natural abundance

#	Name	Isotope labeling	Type	Concentration
1	HIV-1 SL2 stem loop			0.6 ~ 1.2 mM
2	NCp7 protein			0.6 ~ 1.2 mM

Sample #2

#	Name	Isotope labeling	Type	Concentration
3	HIV-1 SL2 stem loop	[U-13C]		0.8 mM
4	NCp7 protein	[U-13C; U-15N]		0.8 mM

Sample #3

#	Name	Isotope labeling	Type	Concentration
5	HIV-1 SL2 stem loop			0.8 ~ 1.2 mM
6	NCp7 protein	[U-15N]		0.8 ~ 1.2 mM

7 1H,1H,13C HCCH-TOCSY

Instrument

#1 Model Bruker Avance DMX (600 MHz)

#2 Model Bruker Avance DRX (800 MHz)

Sample #1

Details natural abundance

#	Name	Isotope labeling	Type	Concentration
1	HIV-1 SL2 stem loop			0.6 ~ 1.2 mM
2	NCp7 protein			0.6 ~ 1.2 mM

Sample #2

#	Name	Isotope labeling	Type	Concentration
3	HIV-1 SL2 stem loop	[U-13C]		0.8 mM
4	NCp7 protein	[U-13C; U-15N]		0.8 mM

Sample #3

#	Name	Isotope labeling	Type	Concentration
5	HIV-1 SL2 stem loop			0.8 ~ 1.2 mM
6	NCp7 protein	[U-15N]		0.8 ~ 1.2 mM

8 1H,1H,15N HSQC-NOESY

Instrument

#1 Model Bruker Avance DMX (600 MHz)

#2 Model Bruker Avance DRX (800 MHz)

Sample #1

Details natural abundance

#	Name	Isotope labeling	Type	Concentration
1	HIV-1 SL2 stem loop			0.6 ~ 1.2 mM
2	NCp7 protein			0.6 ~ 1.2 mM

Sample #2

#	Name	Isotope labeling	Type	Concentration
3	HIV-1 SL2 stem loop	[U-13C]		0.8 mM
4	NCp7 protein	[U-13C; U-15N]		0.8 mM

Sample #3

#	Name	Isotope labeling	Type	Concentration
5	HIV-1 SL2 stem loop			0.8 ~ 1.2 mM
6	NCp7 protein	[U-15N]		0.8 ~ 1.2 mM

nullKeywords HIV-1, NMR assingment, RNA packaging, nucleocapsid protein

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Found 1 Document (1.653 seconds)

BMRB: 4781

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Entries sharing articles BMRB: 1 entries Detail

Related entities 1. HIV-1 SL2 stem loop, : 1 : 1 entities Detail

Related entities 2. NCp7 protein, : 1 : 2 : 12 : 160 entities Detail

Interaction partners 2. NCp7 protein, : 1 interactors Detail

Experiments performed 8 experiments Detail

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