BMRB Entry 27289

Name: Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR and Molecular Dynamics Approach
Published: 2018-02-08

Click here to enlarge.

PDB ID: 6bg9
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR27289
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR and Molecular Dynamics Approach

Deposition date:

2017-10-23

Original release date:

2018-02-08

Authors:

Keane, Sarah; Summers, Michael

Citation:

Citation: Zhang, Kaiming; Keane, Sarah; Zhaoming, Su; Irobalieva, Rossitza; Chen, Muyuan; Van, Verna; Sciandra, Carly; Marchant, Jan; Heng, Xiao; Schmid, Michael; Case, David; Ludtke, Steven; Summers, Michael; Chiu, Wah. "Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach" Structure S0969-2126, 30001-30007 (2018).
PubMed: 29398526

Assembly members:

Assembly members:
DIS, polymer, 47 residues, Formula weight is not available

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: recombinant technology Host organism: in vitro transcription Vector: n/a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DIS: GGCAGGACUCGGCUUGCUGA AGCGCGCACGGCAAGAGGCG AGGGGCC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	214

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DIS	1

Entities:

Entity 1, DIS 47 residues - Formula weight is not available

1

G

C

A

G

A

C

U

C

2

G

C

U

G

C

U

G

A

3

A

G

C

G

C

G

C

A

C

G

4

G

C

A

G

A

G

C

G

5

A

G

C

Samples:

DIS_G8C6r: DIS, G8C6r, 300 uM; TRIS, [U-2H], 20 mM

DIS_H: DIS 300 uM; TRIS, [U-2H], 20 mM

DIS_A2rGr: DIS, A2rGr, 300 uM; TRIS, [U-2H], 20 mM

DIS_A28GH: DIS, A28GH, 300 uM; TRIS, [U-2H], 20 mM

sample_conditions_1: pH: 7.5; pressure: 1 atm; temperature: 308 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	DIS_H	isotropic	sample_conditions_1
2D 1H-1H NOESY	DIS_A2rGr	isotropic	sample_conditions_1
2D 1H-1H NOESY	DIS_A28GH	isotropic	sample_conditions_1
2D 1H-1H NOESY	DIS_G8C6r	isotropic	sample_conditions_1

Software:

NMRView, Johnson, One Moon Scientific - chemical shift assignment, data analysis, processing

TOPSPIN, Bruker Biospin - collection

CYANA, Guntert, Mumenthaler and Wuthrich - geometry optimization

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

NMR spectrometers:

Bruker Avance 600 MHz