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BMRB: 30511

6MCF

Solution structure of 7SK stem-loop 1 with HIV-1 Tat RNA Binding Domain

Authors

Pham, V.V., D'Souza, V.M.

Assembly

Protein Tat/RNA Complex

Entity

1. Protein Tat/RNA Complex, entity 1 (polymer, Thiol state: not present), 57 monomers, 18421.88 Da Detail

GGGAUCUGUC ACCCCAUUGA UCGCCGAGAG GCUGAUCUGG XUGGXUAGGC GGGUCCC

2. Protein Tat/RNA Complex, entity 2 (polymer, Thiol state: not present), 17 monomers, 2153.460 Da Detail

GISYGRKKRR QRRRAHQ

Total weight

20575.34 Da

Max. entity weight

18421.88 Da

Source organism

Homo sapiens , HIV-1 M:B_HXB2R

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.3 %, Completeness: 44.8 %, Completeness (bb): 22.6 % Detail

Polymer type: polyribonucleotide polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	44.8 % (493 of 1100)	52.8 % (320 of 606)	30.2 % (134 of 443)	76.5 % (39 of 51)
Backbone	22.6 % (160 of 707)	24.6 % (90 of 366)	18.5 % (60 of 324)	58.8 % (10 of 17)
Sidechain	84.1 % (343 of 408)	95.8 % (230 of 240)	62.7 % (84 of 134)	85.3 % (29 of 34)
Aromatic	80.5 % (206 of 256)	96.1 % (123 of 128)	57.3 % (55 of 96)	87.5 % (28 of 32)
Methyl	50.0 % (3 of 6)	66.7 % (2 of 3)	33.3 % (1 of 3)

1. entity 1

GGGAUCUGUC ACCCCAUUGA UCGCCGAGAG GCUGAUCUGG XUGGXUAGGC GGGUCCC

2. entity 2

GISYGRKKRR QRRRAHQ

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 100000 Pa, Temperature 298 K, pH 5.4, Details 0.5 mM 7SK Stem-loop 1 RNA, 0.5 mM [U-13C; U-15N] HIV-1 Tat RNA Binding Domain selectively labeled with the following schema: 1) R49, K50, R57, A58 2) K51, R52, Q54, R55 3) R53, Q54, R56, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	7SK Stem-loop 1 RNA	natural abundance	0.5 (±0.1) mM
2	HIV-1 Tat RNA Binding Domain	[U-13C; U-15N]	0.5 (±0.1) mM
3	phosphates	natural abundance	10 mM
4	NaCl	natural abundance	70 mM

Sample #2

Solvent system 100% D2O, Pressure 100000 Pa, Temperature 298 K, pH 5.4, Details 0.5 mM 7SK Stem-loop 1 RNA, 0.5 mM HIV-1 Tat RNA Binding Domain, 100% D2O

#	Name	Isotope labeling	Concentration
5	7SK Stem-loop 1 RNA	natural abundance	0.5 (±0.1) mM
6	HIV-1 Tat RNA Binding Domain	natural abundance	0.5 (±0.1) mM
7	phosphates	natural abundance	10 mM
8	NaCl	natural abundance	70 mM

Sample #3

Solvent system 100% D2O, Pressure 100000 Pa, Temperature 298 K, pH 5.4, Details 0.5 mM 7SK Stem-loop 1 RNA, 0.5 mM [U-13C; U-15N] HIV-1 Tat RNA Binding Domain selectively labeled with the following schema: 1) R49, K50, R57, A58 2) K51, R52, Q54, R55 3) R53, Q54, R56, 100% D2O

#	Name	Isotope labeling	Concentration
9	7SK Stem-loop 1 RNA	natural abundance	0.5 (±0.1) mM
10	HIV-1 Tat RNA Binding Domain	[U-13C; U-15N]	0.5 (±0.1) mM
11	phosphates	natural abundance	10 mM
12	NaCl	natural abundance	70 mM

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 100000 Pa, Temperature 298 K, pH 5.4, Details 0.5 mM [U-13C; U-15N] 7SK Stem-loop 1 RNA, 0.5 mM HIV-1 Tat RNA Binding Domain, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
13	7SK Stem-loop 1 RNA	[U-13C; U-15N]	0.5 (±0.1) mM
14	HIV-1 Tat RNA Binding Domain	natural abundance	0.5 (±0.1) mM
15	phosphates	natural abundance	10 mM
16	NaCl	natural abundance	70 mM

Sample #5

Solvent system 100% D2O, Pressure 100000 Pa, Temperature 298 K, pH 5.4, Details 0.5 mM [U-13C; U-15N] 7SK Stem-loop 1 RNA, 0.5 mM HIV-1 Tat RNA Binding Domain, 100% D2O

#	Name	Isotope labeling	Concentration
17	7SK Stem-loop 1 RNA	[U-13C; U-15N]	0.5 (±0.1) mM
18	HIV-1 Tat RNA Binding Domain	natural abundance	0.5 (±0.1) mM
19	phosphates	natural abundance	10 mM
20	NaCl	natural abundance	70 mM

Sample #6

Solvent system 90% H2O/10% D2O, Pressure 100000 Pa, Temperature 298 K, pH 5.4, Details 0.5 mM 7SK Stem-loop 1 RNA, 0.5 mM HIV-1 Tat RNA Binding Domain, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
21	7SK Stem-loop 1 RNA	natural abundance	0.5 (±0.1) mM
22	HIV-1 Tat RNA Binding Domain	natural abundance	0.5 (±0.1) mM
23	phosphates	natural abundance	10 mM
24	NaCl	natural abundance	70 mM

Release date

2018-10-04

Citation

HIV-1 Tat interactions with cellular 7SK and viral TAR RNAs identifies dual structural mimicry
Pham, V.V., Salguero, C., Khan, S.N., Meagher, J., Brown, W., Humbert, N., de Rocquigny, H., Smith, J., D'Souza, V.M.
Nat. Commun. (2018), 9, 4266-4266, PubMed 30323330 , DOI 10.1038/s41467-018-06591-6 , Abstract

Entries sharing articles BMRB: 2 entries Detail

  BMRB: 30510 released on 2018-09-09
    Title Solution structure of HIV-1 TAR with Tat RNA Binding Domain
  BMRB: 30512 released on 2018-09-09
    Title Solution structure of 7SK stem-loop 1

Related entities 1. Protein Tat/RNA Complex, entity 1, : 1 : 1 : 4 : 3 entities Detail

Related entities 2. Protein Tat/RNA Complex, entity 2, : 1 : 5 : 6 : 4 entities Detail

Interaction partners 2. Protein Tat/RNA Complex, entity 2, : 20 interactors Detail

More details for 20 interactors identified by 7 citations

Experiments performed 6 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker DMX - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 100000 Pa, Temperature 298 K, pH 5.4, Details 0.5 mM 7SK Stem-loop 1 RNA, 0.5 mM HIV-1 Tat RNA Binding Domain, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
21	7SK Stem-loop 1 RNA	natural abundance	0.5 (±0.1) mM
22	HIV-1 Tat RNA Binding Domain	natural abundance	0.5 (±0.1) mM
23	phosphates	natural abundance	10 mM
24	NaCl	natural abundance	70 mM

2 2D 1H-15N HSQC

Instrument

Bruker DMX - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 100000 Pa, Temperature 298 K, pH 5.4, Details 0.5 mM 7SK Stem-loop 1 RNA, 0.5 mM [U-13C; U-15N] HIV-1 Tat RNA Binding Domain selectively labeled with the following schema: 1) R49, K50, R57, A58 2) K51, R52, Q54, R55 3) R53, Q54, R56, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	7SK Stem-loop 1 RNA	natural abundance	0.5 (±0.1) mM
2	HIV-1 Tat RNA Binding Domain	[U-13C; U-15N]	0.5 (±0.1) mM
3	phosphates	natural abundance	10 mM
4	NaCl	natural abundance	70 mM

3 2D 1H-15N HSQC

Instrument

Bruker DMX - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 100000 Pa, Temperature 298 K, pH 5.4, Details 0.5 mM [U-13C; U-15N] 7SK Stem-loop 1 RNA, 0.5 mM HIV-1 Tat RNA Binding Domain, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
13	7SK Stem-loop 1 RNA	[U-13C; U-15N]	0.5 (±0.1) mM
14	HIV-1 Tat RNA Binding Domain	natural abundance	0.5 (±0.1) mM
15	phosphates	natural abundance	10 mM
16	NaCl	natural abundance	70 mM

4 2D 1H-13C HSQC

Instrument

Bruker DMX - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 100000 Pa, Temperature 298 K, pH 5.4, Details 0.5 mM 7SK Stem-loop 1 RNA, 0.5 mM [U-13C; U-15N] HIV-1 Tat RNA Binding Domain selectively labeled with the following schema: 1) R49, K50, R57, A58 2) K51, R52, Q54, R55 3) R53, Q54, R56, 100% D2O

#	Name	Isotope labeling	Concentration
9	7SK Stem-loop 1 RNA	natural abundance	0.5 (±0.1) mM
10	HIV-1 Tat RNA Binding Domain	[U-13C; U-15N]	0.5 (±0.1) mM
11	phosphates	natural abundance	10 mM
12	NaCl	natural abundance	70 mM

5 2D 1H-1H NOESY

Instrument

Bruker DMX - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 100000 Pa, Temperature 298 K, pH 5.4, Details 0.5 mM 7SK Stem-loop 1 RNA, 0.5 mM HIV-1 Tat RNA Binding Domain, 100% D2O

#	Name	Isotope labeling	Concentration
5	7SK Stem-loop 1 RNA	natural abundance	0.5 (±0.1) mM
6	HIV-1 Tat RNA Binding Domain	natural abundance	0.5 (±0.1) mM
7	phosphates	natural abundance	10 mM
8	NaCl	natural abundance	70 mM

6 2D 1H-13C HSQC

Instrument

Bruker DMX - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 100000 Pa, Temperature 298 K, pH 5.4, Details 0.5 mM [U-13C; U-15N] 7SK Stem-loop 1 RNA, 0.5 mM HIV-1 Tat RNA Binding Domain, 100% D2O

#	Name	Isotope labeling	Concentration
17	7SK Stem-loop 1 RNA	[U-13C; U-15N]	0.5 (±0.1) mM
18	HIV-1 Tat RNA Binding Domain	natural abundance	0.5 (±0.1) mM
19	phosphates	natural abundance	10 mM
20	NaCl	natural abundance	70 mM

nullKeywords RNA BINDING PROTEIN, RNA Binding Domain, Transcription

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Found 1 Document (0.723 seconds)

BMRB: 30511

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Sample #5

Sample #6

Entries sharing articles BMRB: 2 entries Detail

Related entities 1. Protein Tat/RNA Complex, entity 1, : 1 : 1 : 4 : 3 entities Detail

Related entities 2. Protein Tat/RNA Complex, entity 2, : 1 : 5 : 6 : 4 entities Detail

Interaction partners 2. Protein Tat/RNA Complex, entity 2, : 20 interactors Detail

Experiments performed 6 experiments Detail

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