BMRB Entry 16941

Name: Recognition of HIV TAR RNA by peptide mimetic of Tat protein
Published: 2010-08-24

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PDB ID: 2kx5
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR16941
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Recognition of HIV TAR RNA by peptide mimetic of Tat protein PubMed: 20724442

Deposition date: 2010-05-20 Original release date: 2010-08-24

Authors: Davidson, Amy; Patora-Komisarska, Krystyna; Robinson, John; Varani, Gabriele

Citation: Davidson, Amy; Patora-Komisarska, Krystyna; Robinson, John; Varani, Gabriele. "Essential structural requirements for specific recognition of HIV TAR RNA by peptide mimetics of Tat protein." Nucleic Acids Res. 39, 248-256 (2011).

Assembly members:
HIV-1_TAR/KP-Z-41, polymer, 29 residues, 11193.474 Da.
peptide, polymer, 18 residues, Formula weight is not available

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

Experimental source: Production method: in vitro transcription

Entity Sequences (FASTA):
HIV-1_TAR/KP-Z-41: GGCAGAUCUGAGCCUGGGAG CUCUCUGCC
peptide: RVRCRQRKGRRICIRIXP

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	275

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA/RNA (47-MER)	1
2	peptide	2

Entities:

Entity 1, DNA/RNA (47-MER) 29 residues - 11193.474 Da.

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, peptide 18 residues - Formula weight is not available

1

ARG

VAL

ARG

CYS

ARG

GLN

ARG

LYS

GLY

ARG

2

ARG

ILE

CYS

ILE

ARG

ILE

DPR

PRO

Samples:

sample_1: HIV-1 TAR/KP-Z-41 1 mM; D2O 100%

sample_2: HIV-1 TAR/KP-Z-41 1 mM; H2O 90%; D2O 10%

sample_3: HIV-1 TAR/KP-Z-41, [U-98% 13C; U-98% 15N], 1 mM; D2O 100%

sample_4: HIV-1 TAR/KP-Z-41, [U-2H], 1 mM; D2O 100%

sample_5: HIV-1 TAR/KP-Z-41, [U-98% 13C; U-98% 15N], 1 mM; H2O 90%; D2O 10%

sample_conditions_2: ionic strength: 0.01 M; pH: 6.6; pressure: 1 atm; temperature: 277 K

sample_conditions_1: ionic strength: 0.01 M; pH: 6.6; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_3	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_3	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_4	isotropic	sample_conditions_1
2D F1fF2f NOESY	sample_3	isotropic	sample_conditions_1
2D F1fF2f NOESY	sample_5	isotropic	sample_conditions_2
2D F1fF2f TOCSY	sample_3	isotropic	sample_conditions_1

Software:

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution

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

SPARKY, Goddard - chemical shift assignment, peak picking

NMR spectrometers:

Bruker DRX 500 MHz
Bruker DMX 600 MHz

Biological Magnetic Resonance Data Bank