BMRB Entry 16877

Name: Simultaneous recognition of HIV-1 TAR RNA bulge and loop sequences by cyclic peptide mimics of Tat protein
Published: 2010-04-29

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR16877

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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:

Simultaneous recognition of HIV-1 TAR RNA bulge and loop sequences by cyclic peptide mimics of Tat protein

Deposition date:

2010-04-16

Original release date:

2010-04-29

Authors:

Davidson, Amy; Leeper, Thomas; Varani, Gabriele

Citation:

Citation: Davidson, Amy; Leeper, Thomas; Athanassiou, Zafiria; Patora-Komisarska, Krystyna; Karn, Jonathan; Robinson, John; Varani, Gabriele. "Simultaneous recognition of HIV-1 TAR RNA bulge and loop sequences by cyclic peptide mimics of Tat protein." Proc. Natl. Acad. Sci. U.S.A. 106, 11931-11936 (2009).
PubMed: 19584251

Assembly members:

Assembly members:
TAR, polymer, 29 residues, Formula weight is not available
TAT, polymer, 14 residues, Formula weight is not available

Natural source:

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

Experimental source:

Experimental source: Production method: enzymatic semisynthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
TAR: GGCAGAUCUGAGCCUGGGAG CUCUCUGCC
TAT: RVRTRKGRRIRIPP

Data sets:

assigned_chemical_shifts
- L22-TAR_non-exchangeable_hydrogen

Data type	Count
1H chemical shifts	330

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	TAR RNA bulge	1
2	Tat protein	2

Entities:

Entity 1, TAR RNA bulge 29 residues - Formula weight is not available

1

G

C

A

G

A

U

C

U

G

2

A

G

C

U

G

A

G

3

C

U

C

U

C

U

G

C

Entity 2, Tat protein 14 residues - Formula weight is not available

1

ARG

VAL

ARG

THR

ARG

LYS

GLY

ARG

ILE

2

ARG

ILE

PRO

Samples:

sample_1: HIV-1 TAR RNA 1.0 ± 0.1 mM; L-22 peptide 1.0 ± 0.2 mM; D2O 100%; potassium phosphate 10 mM

sample_2: HIV-1 TAR RNA 1.0 ± 0.1 mM; L-22 peptide 1.0 ± 0.2 mM; D2O 10%; potassium phosphate 10 mM; H2O 90%

sample_3: HIV-1 TAR RNA, [U-98% 13C; U-98% 15N], 1.0 ± 0.1 mM; L-22 peptide 1.0 ± 0.2 mM; D2O 100%; potassium phosphate 10 mM

sample_4: HIV-1 TAR RNA, [U-98% 13C; U-98% 15N], 1.0 ± 0.1 mM; L-22 peptide 1.0 ± 0.2 mM; D2O 10%; potassium phosphate 10 mM; H2O 90%

sample_5: HIV-1 TAR RNA, [U-2H], 1.0 ± 0.2 mM; L-22 peptide 1.0 ± 0.2 mM; D2O 100%; potassium phosphate 10 mM

sample_conditions_1: ionic strength: 10 mM; pH: 6.6; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 10 mM; pH: 6.6; pressure: 1 atm; temperature: 277 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D-13C HMQC NOESY	sample_3	isotropic	sample_conditions_1
3D HCCH TOCSY	sample_3	isotropic	sample_conditions_1
IPAP-HSQC	sample_3	isotropic	sample_conditions_1
15N HSQC	sample_4	isotropic	sample_conditions_2
2D noesy	sample_1	isotropic	sample_conditions_1
2D watergate NOESY	sample_2	isotropic	sample_conditions_2
F1fF2f-type noesy	sample_3	isotropic	sample_conditions_1
F1fF2f-type tocsy	sample_3	isotropic	sample_conditions_1
2D HCCH-COSY	sample_3	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_5	isotropic	sample_conditions_1
F1fF2f-type watergate noesy	sample_4	isotropic	sample_conditions_2

Software:

X-PLOR NIH v2.16.0, C.D. Schwieters, J.J. Kuszewski, N. Tjandra and G.M. Clore - structure solution

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

TOPSPIN, Bruker Biospin - collection

TALOS, Cornilescu, Delaglio and Bax - data analysis

SPARKY, Goddard - peak picking

NMR spectrometers:

Bruker DRX 500 MHz
Bruker DMX 600 MHz
Varian Inova 800 MHz
Bruker AVIII 600 MHz