BMRB Entry 30817

Name: Ax1 Domain of VEGF Readthrough Element
Published: 2022-05-26

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PDB ID: 7kuc
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30817
MolProbity Validation Chart

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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:

Ax1 Domain of VEGF Readthrough Element

Deposition date:

2020-11-24

Original release date:

2022-05-26

Authors:

D'Souza, V.; Wagner, N.; Edwards, J.

Citation:

Citation: Wagner, N.; Edwards, J.; Abramovich, J.; Gupta, P.; Swaminathan, H.; Rouskin, S.; D'Souza, V.. "Stop codon readthrough in VEGF-A is regulated by complex signals" .

Assembly members:

Assembly members:
entity_1, polymer, 16 residues, 5215.198 Da.

Natural source:

Natural source: Common Name: cow Taxonomy ID: 9913 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Bos taurus

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GGAGGAAGGAGCCUCC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list

Data type	Count
13C chemical shifts	41
1H chemical shifts	94

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 16 residues - 5215.198 Da.

1

G

A

G

A

G

A

2

G

C

U

C

Samples:

sample_1: RNA 1 ± 0.2 mM; KCL 50 mM

sample_2: RNA, [U-13C], 1 ± 0.2 mM; KCL 50 mM

sample_3: RNA 1 ± 0.2 mM; KCL 50 mM

sample_conditions_1: ionic strength: 50 mM; pH: 5.6; pressure: 1 .; temperature: 311 K

sample_conditions_2: ionic strength: 50 mM; pH: 5.6; pressure: 1 .; temperature: 311 K

sample_conditions_3: ionic strength: 50 mM; pH: 5.6; pressure: 1 .; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D_NOESY	sample_1	anisotropic	sample_conditions_1
1H-13C_HMQC	sample_2	anisotropic	sample_conditions_2
2D_NOESY	sample_3	anisotropic	sample_conditions_3

Software:

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

NMRViewJ, Bruce A. Johnson - chemical shift assignment

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

X-PLOR NIH v3.1, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

Bruker Ascend800 800 MHz
Bruker UltraShield700Plus 700 MHz