BMRB Entry 15915

Name: NMR structure of the human tRNALys3 bound to the HIV genome Loop I
Published: 2008-09-30

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PDB ID: 2k7e
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR15915
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR structure of the human tRNALys3 bound to the HIV genome Loop I

Deposition date:

2008-08-09

Original release date:

2008-09-30

Authors:

Bilbille, Yann; Vendeix, Franck; Guenther, Richard; Malkiewicz, Andrzej; Ariza, Xavier; Vilarrasa, Jaume; Agris, Paul

Citation:

Citation: Bilbille, Yann; Vendeix, Franck; Guenther, Richard; Malkiewicz, Andrzej; Ariza, Xavier; Vilarrasa, Jaume; Agris, Paul. "The structure of the human tRNALys3 anticodon bound to the HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs" Nucleic Acids Res. 37, 3342-3353 (2009).
PubMed: 19324888

Assembly members:

Assembly members:
RNA_(5'-R(*GP*CP*GP*GP*UP*GP*UP*AP*AP*AP*AP*G)-3'), polymer, 12 residues, 3915.436 Da.
T-RNA_(5'-R(*CP*UP*(2SU)P*UP*UP*AP*AP*(PSU)P*CP*UP*GP*C)-3'), polymer, 12 residues, 3386.044 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_(5'-R(*GP*CP*GP*GP*UP*GP*UP*AP*AP*AP*AP*G)-3'): GCGGUGUAAAAG
T-RNA_(5'-R(*CP*UP*(2SU)P*UP*UP*AP*AP*(PSU)P*CP*UP*GP*C)-3'): CUXUUAAXCUGC

Data sets:

assigned_chemical_shifts

Data type	Count
1H chemical shifts	252

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (5'-R(GPCPGPGPUPGPUPAPAPAPAPG)-3')	1
2	T-RNA (5'-R(CPUP(2SU)PUPUPAPAP(PSU)PCPUPGPC)-3')	2

Entities:

Entity 1, RNA (5'-R(*GP*CP*GP*GP*UP*GP*UP*AP*AP*AP*AP*G)-3') 12 residues - 3915.436 Da.

1

G

C

G

U

G

U

A

2

A

G

Entity 2, T-RNA (5'-R(*CP*UP*(2SU)P*UP*UP*AP*AP*(PSU)P*CP*UP*GP*C)-3') 12 residues - 3386.044 Da.

1

C

U

2SU

U

A

PSU

C

U

2

G

C

Samples:

vgps-H2O_D2O: RNA (5'-R(*GP*CP*GP*GP*UP*GP*UP*AP*AP*AP*AP*G)-3') 0.3-1.2 mM; T-RNA (5'-R(*CP*UP*(2SU)P*UP*UP*AP*AP*(PSU)P*CP*UP*GP*C)-3') 0.3-1.2 mM; sodium phosphate 10 mM; sodium chloride 100 mM; H2O 90%; D2O, [U-100% 2H], 10%

vgps-D2O: RNA (5'-R(*GP*CP*GP*GP*UP*GP*UP*AP*AP*AP*AP*G)-3') 0.3-1.2 mM; T-RNA (5'-R(*CP*UP*(2SU)P*UP*UP*AP*AP*(PSU)P*CP*UP*GP*C)-3') 0.3-1.2 mM; sodium phosphate 10 mM; sodium chloride 100 mM; D2O, [U-100% 2H], 100%

sample_conditions_276: ionic strength: 100 mM; pH: 6.5; pressure: 1 atm; temperature: 276 K

sample_conditions_293: ionic strength: 100 mM; pH: 6.5; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	vgps-H2O_D2O	isotropic	sample_conditions_276
2D 1H-1H NOESY	vgps-H2O_D2O	isotropic	sample_conditions_293
2D 1H-13C HSQC	vgps-D2O	isotropic	sample_conditions_293
2D DQF-COSY	vgps-D2O	isotropic	sample_conditions_293
2D 1H-1H NOESY	vgps-D2O	isotropic	sample_conditions_293
2D 1H-15N HSQC	vgps-H2O_D2O	isotropic	sample_conditions_276

Software:

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

SPARKY, Goddard - chemical shift assignment

Molmol, Koradi, Billeter and Wuthrich - data analysis

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

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

NMRView, Johnson, One Moon Scientific - data analysis

xwinnmr, Bruker Biospin - collection

NMR spectrometers:

Bruker Avance 500 MHz
Varian INOVA 600 MHz