BMRB Entry 51144

Name: RNA modifications stabilize the tertiary structure of tRNAfMet by locally increasing conformational dynamics
Published: 2022-01-20

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR51144

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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:

RNA modifications stabilize the tertiary structure of tRNAfMet by locally increasing conformational dynamics

Deposition date:

2021-10-16

Original release date:

2022-01-20

Authors:

Biedenbander, Thomas; de Jesus, Vanessa; Schmidt-Dengler, Martina; Helm, Mark; Corzilius, Bjoern; Fuertig, Boris

Citation:

Citation: Biedenbander, Thomas; de Jesus, Vanessa; Schmidt-Dengler, Martina; Helm, Mark; Corzilius, Bjorn; Furtig, Boris. "RNA modifications stabilize the tertiary structure of tRNAfMet by locally increasing conformational dynamics" Nucleic Acids Res. 50, 2334-2349 (2022).
PubMed: 35137185

Assembly members:

Assembly members:
entity_1, polymer, 77 residues, Formula weight is not available

Natural source:

Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli

Experimental source:

Experimental source: Production method: purified from the natural source

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: CGCGGGGXGGAGCAGCCUGG XAGCUCGUCGGGXUCAUAAC CCGAAGAUCGUCGGXXCAAA UCCGGCCCCCGCAACCA

Data sets:

H_exch_rates
assigned_chemical_shifts
- assigned_chemical_shifts_1
heteronucl_NOEs
- heteronucl_NOEs_1
- heteronucl_NOEs_2
heteronucl_T1_relaxation
- heteronucl_T1_relaxation_1
- heteronucl_T1_relaxation_2
heteronucl_T2_relaxation
- heteronucl_T2_relaxation_1
- heteronucl_T2_relaxation_2

Data type	Count
13C chemical shifts	4
15N chemical shifts	28
1H chemical shifts	34
H exchange rates	183
T1 relaxation values	51
T2 relaxation values	49
heteronuclear NOE values	52

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	tRNAfMet	1

Entities:

Entity 1, tRNAfMet 77 residues - Formula weight is not available

1

C

G

C

G

4SU

G

2

A

G

C

A

G

C

U

G

3

H2U

A

G

C

U

C

G

U

C

G

4

G

OMC

U

C

A

U

A

C

5

C

G

A

G

A

U

C

G

6

U

C

G

5MU

PSU

C

A

7

U

C

G

C

8

G

C

A

C

A

Samples:

sample_1: tRNAfMet, [U-100% 13C; U-100% 15N], 530 uM; H2O 93%; D2O, [U-100% 2H], 7%; DSS 250 mM; potassium phosphate 25 mM; potassium chloride 200 mM

sample_conditions_1: ionic strength: 0.2 M; pH: 6.4; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 0.2 M; pH: 6.4; pressure: 1 atm; temperature: 310 K

sample_conditions_3: ionic strength: 0.2 M; pH: 6.4; pressure: 1 atm; temperature: 290 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N TROSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D 15N-separated NOESY	sample_1	isotropic	sample_conditions_1
T1/R1 relaxation	sample_1	isotropic	sample_conditions_1
T1/R1 relaxation	sample_1	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_3
T2/R2 relaxation	sample_1	isotropic	sample_conditions_1
T2/R2 relaxation	sample_1	isotropic	sample_conditions_2
1H-15N heteronoe	sample_1	isotropic	sample_conditions_1
1H-15N heteronoe	sample_1	isotropic	sample_conditions_2
2D-HNN-COSY	sample_1	isotropic	sample_conditions_1
2D water selective inversion recovery	sample_1	isotropic	sample_conditions_1

Software:

NMRbox v7.0 - data analysis

DynamicsCenter v2.6 - data analysis

SPARKY v3.114 - chemical shift assignment

TOPSPIN v3.2 - processing

ChimeraX v1.2.5 - Structure visualization

Relax v4.1.3 - data analysis

NMR spectrometers:

Bruker Avance 600 MHz
Bruker AVANCE NEO 600 MHz
Bruker AVANCE NEO 900 MHz
Bruker AVANCE III 950 MHz
Bruker AVANCE III 800 MHz
Bruker Avance 800 MHz