BMRB Entry 30452

Name: Solution structure of a ultra-high affinity macrocycle bound to HIV-1 TAR RNA
Published: 2018-12-04

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PDB ID: 6d2u
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30452
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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:

Solution structure of a ultra-high affinity macrocycle bound to HIV-1 TAR RNA

Deposition date:

2018-04-13

Original release date:

2018-12-04

Authors:

Shortridge, M.; Varani, G.

Citation:

Citation: Shortridge, M.; Wille, P.; Jones, A.; Davidson, A.; Bogdanovic, J.; Arts, E.; Karn, J.; Robinson, J.; Varani, G.. "An ultra-high affinity ligand of HIV-1 TAR reveals the RNA structure recognized by P-TEFb" Nucleic Acids Res. 47, 1523-1531 (2019).
PubMed: 30481318

Assembly members:

Assembly members:
entity_1, polymer, 14 residues, 1697.087 Da.
entity_2, polymer, 29 residues, 9307.555 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: recombinant technology Host organism: synthetic construct

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: XVRTRKGRRIXIXP
entity_2: GGCAGAUCUGAGCCUGGGAG CUCUCUGCC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
- assigned_chemical_shifts_2

Data type	Count
13C chemical shifts	171
15N chemical shifts	11
1H chemical shifts	338

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2

Entities:

Entity 1, entity_1 14 residues - 1697.087 Da.

1

DAB

VAL

ARG

THR

ARG

LYS

GLY

ARG

ILE

2

4J5

ILE

DPR

PRO

Entity 2, entity_2 29 residues - 9307.555 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

Samples:

sample_1: DAB-VAL-ARG-THR-ARG-LYS-GLY-ARG-ARG-ILE-NOR-ILE-DPR-PRO 1.7 mM; RNA (29-MER) 1.2 mM; EDTA 0.01 mM; potassium phosphate 20 mM; sodium chloride 10 mM

sample_2: DAB-VAL-ARG-THR-ARG-LYS-GLY-ARG-ARG-ILE-NOR-ILE-DPR-PRO 1.7 mM; RNA (29-MER) 1.2 mM; EDTA 0.01 mM; potassium phosphate 20 mM; sodium chloride 10 mM

sample_3: DAB-VAL-ARG-THR-ARG-LYS-GLY-ARG-ARG-ILE-NOR-ILE-DPR-PRO 1.5 mM; RNA (29-MER), [U-99% 13C; U-99% 15N], 1.0 mM; EDTA 0.01 mM; potassium phosphate 20 mM; sodium chloride 10 mM

sample_4: DAB-VAL-ARG-THR-ARG-LYS-GLY-ARG-ARG-ILE-NOR-ILE-DPR-PRO 1.5 mM; RNA (29-MER), [U-99% 13C; U-99% 15N], 1.0 mM; EDTA 0.01 mM; potassium phosphate 20 mM; sodium chloride 10 mM

sample_conditions_1: ionic strength: 30 mM; pH: 6.5; pressure: 1 atm; temperature: 277 K

sample_conditions_2: ionic strength: 30 mM; pH: 6.5; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_4	isotropic	sample_conditions_2
3D 1H-15N NOESY	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_4	isotropic	sample_conditions_2

Software:

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

SPARKY, Goddard - chemical shift assignment, peak picking

NMR spectrometers:

Bruker DRX 500 MHz
Bruker AvanceII 600 MHz
Bruker AvanceIII 800 MHz