BMRB Entry 30049

Name: Excited state (Bound-like) sampled during RDC restrained Replica-averaged Metadynamics (RAM) simulations of the HIV-1 TAR complexed with cyclic peptide mimetic of Tat
Published: 2016-06-06

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PDB ID: 5j1o
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30049
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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:

Excited state (Bound-like) sampled during RDC restrained Replica-averaged Metadynamics (RAM) simulations of the HIV-1 TAR complexed with cyclic peptide mimetic of Tat

Deposition date:

2016-03-29

Original release date:

2016-06-06

Authors:

Borkar, A.; Bardaro, M.; Varani, G.; Vendrucolo, M.

Citation:

Citation: Borkar, A.; Bardaro, M.; Camilloni, C.; Aprile, F.; Varani, G.; Vendrucolo, M.. "Structure of a low-population binding intermediate in protein-RNA recognition" Proc. Natl. Acad. Sci. U. S. A. 113, 7171-7176 (2016).
PubMed: 7286828

Assembly members:

Assembly members:
Cyclic peptide mimetic of Tat, polymer, 14 residues, 1768.189 Da.
Apical region (29mer) of the HIV-1 TAR RNA element, polymer, 29 residues, 9307.555 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Cyclic peptide mimetic of Tat: RVRTRKGRRIRIXP
Apical region (29mer) of the HIV-1 TAR RNA element: GGCAGAUCUGAGCCUGGGAG CUCUCUGCC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
- assigned_chemical_shifts_2

Data type	Count
13C chemical shifts	162
1H chemical shifts	389

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 - 1768.189 Da.

1

ARG

VAL

ARG

THR

ARG

LYS

GLY

ARG

ILE

2

ARG

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: RNA and peptide, [U-99% 13C; U-99% 15N], 2 uM; D2O 100%

sample_conditions_1: ionic strength: 150 mM; pH: 6.6; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
RDC	sample_1	anisotropic	sample_conditions_1

Software:

Gromacs and Plumed, Vendruscolo, Camilloni and Borkar - structure calculation

NMR spectrometers:

Varian INOVA 800 MHz