BMRB Entry 16431

Name: Complex of HIV-2 TAR RNA and a synthetic tripeptide in a 1:2 stoichiometry
Published: 2009-09-08

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PDB ID: 2kmj
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR16431
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Complex of HIV-2 TAR RNA and a synthetic tripeptide in a 1:2 stoichiometry PubMed: 19444830

Deposition date: 2009-07-30 Original release date: 2009-09-08

Authors: Ferner, Jan; Suhartono, Marcel; Breitung, Sven; Jonker, Hendrik; Hennig, Mirko; Woehnert, Jens; Goebel, Michael; Schwalbe, Harald

Citation: Ferner, Jan; Suhartono, Marcel; Breitung, Sven; Jonker, Hendrik; Hennig, Mirko; Woehnert, Jens; Goebel, Michael; Schwalbe, Harald. "Structures of HIV TAR RNA-ligand complexes reveal higher binding stoichiometries" ChemBioChem 10, 1490-1494 (2009).

Assembly members:
UUCG-TAR, polymer, 28 residues, Formula weight is not available
Pyrimidinylpeptide, polymer, 3 residues, Formula weight is not available

Natural source: Common Name: AIDS virus Taxonomy ID: 11709 Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):
UUCG-TAR: GGCCAGAUUGAGCUUCGGCU CUCUGGUC
Pyrimidinylpeptide: XXX

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	172
15N chemical shifts	57
1H chemical shifts	236

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	UUCG-TAR	1
2	LIG1	2
3	LIG2	2

Entities:

Entity 1, UUCG-TAR 28 residues - Formula weight is not available

1

G

C

A

G

A

U

G

2

A

G

C

U

C

G

C

U

3

C

U

C

U

G

U

C

Entity 2, LIG1 3 residues - Formula weight is not available

2X=PPA (2-amino-5-(pyrimidin-2-yl)pentanoic acid)

1

DAR

PPA

DAR

Samples:

sample_1: UUCG-TAR, [U-100% 13C; U-100% 15N], 0.65 mM; Pyrimidinylpeptide 5.2 mM; potassium chloride 50 mM; potassium phosphate 25 mM; H2O 90%; D2O 10%

sample_2: UUCG-TAR, [U-100% 13C; U-100% 15N], 0.65 mM; Pyrimidinylpeptide 5.2 mM; potassium chloride 50 mM; potassium phosphate 25 mM; D2O 100%

sample_3: UUCG-TAR 0.65 mM; Pyrimidinylpeptide 5.2 mM; potassium chloride 50 mM; potassium phosphate 25 mM; H2O 90%; D2O 10%

sample_4: UUCG-TAR 0.65 mM; Pyrimidinylpeptide 5.2 mM; potassium chloride 50 mM; potassium phosphate 25 mM; D2O 100%

sample_5: UUCG-TAR, [U-100% 13C; U-100% 15N], 0.2 mM; Pyrimidinylpeptide 0.8 mM; potassium chloride 50 mM; potassium phosphate 25 mM; Pf1 phage 16 mg/mL; D2O 100%

sample_conditions_1: ionic strength: 75 mM; pH: 6.2; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 75 mM; pH: 6.2; pressure: 1 atm; temperature: 283 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_3	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_3	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_4	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D HCCH-COSY	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_2
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
2D H(C)N	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC (2J)	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	anisotropic	sample_conditions_1
2D HNN-COSY	sample_1	isotropic	sample_conditions_2
2D H5NN-COSY	sample_2	isotropic	sample_conditions_1
3D forward-directed HCC-TOCSY-CCH E.COSY	sample_2	isotropic	sample_conditions_1
2D 1H-15N CPMG-NOESY	sample_1	isotropic	sample_conditions_2

Software:

TOPSPIN v2.1, Bruker Biospin - collection, data analysis, processing

SPARKY v3.114, Goddard - chemical shift assignment, data analysis, peak picking

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

ARIA v1.2, Linge, O'Donoghue and Nilges - refinement

HADDOCK v2.1, Dominguez, Boelens and Bonvin - refinement

NMR spectrometers:

Bruker Avance 900 MHz
Bruker Avance 800 MHz
Bruker Avance 700 MHz
Bruker Avance 600 MHz
Bruker DRX 600 MHz
Bruker Avance 400 MHz