Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR52000

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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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Name: RNA aptazyme apo
Published: 2026-02-23

Title:

RNA aptazyme apo

Deposition date:

2023-06-15

Original release date:

2026-02-23

Authors:

Lee, Yun-Tzai

Citation:

Citation: Stagno, Jason; Deme, Justin; Dwivedi, Vibha; Lee, Yun-Tzai; Lee, Hyun Kyung; Yu, Ping; Chen, Szu-Yun; Fan, Lixin; Degenhardt, Maximilia; Chari, Raj; Young, Howard; Lea, Susan; Wang, Yun-Xing. "Structural investigation of an RNA device that regulates PD-1 expression in mammalian cells" Nucleic Acids Res. 53, gkaf156-gkaf156 (2025).
PubMed: 40071935

Assembly members:

Assembly members:
entity_1, polymer, 108 residues, Formula weight is not available
entity_MG, non-polymer, 24.305 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: in vitro transcription Host organism: not applicable

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GCAGGUACAUCCAGCUGAUG AGUCCCAAAUAGGACAAAAA GGGAGAGGUGAAGAAUACGA CCACCUAGGCUCGAAAGAGC CUAAAACAUACCUUUCCUGG AUUCCUGC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
- assigned_chemical_shifts_2

Data type	Count
15N chemical shifts	82
1H chemical shifts	46

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA aptazyme device	1
2	Magnesium ion, 1	2
3	Magnesium ion, 2	2
4	Magnesium ion, 3	2
5	Magnesium ion, 4	2
6	Magnesium ion, 5	2
7	Magnesium ion, 6	2
8	Magnesium ion, 7	2
9	Magnesium ion, 8	2
10	Magnesium ion, 9	2
11	Magnesium ion, 10	2
12	Magnesium ion, 11	2
13	Magnesium ion, 12	2

Entities:

Entity 1, RNA aptazyme device 108 residues - Formula weight is not available

1

G

C

A

G

U

A

C

A

U

2

C

A

G

C

U

G

A

U

G

3

A

G

U

C

A

U

4

A

G

A

C

A

5

G

A

G

A

G

U

G

6

A

G

A

U

A

C

G

A

7

C

A

C

U

A

G

C

8

U

C

G

A

G

A

G

C

9

C

U

A

C

A

U

A

10

C

U

C

U

G

11

A

U

C

U

G

C

Entity 2, Magnesium ion, 1 - Mg - 24.305 Da.

1

MG

Samples:

sample_1: RNA aptazyme apo-state, [U-100% 15N], 250 uM; Potassium chloride 50 mM; Magnesium chloride 1 mM

sample_conditions_1: ionic strength: 0.15 M; pH: 6.5; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D HNN COSY	sample_1	isotropic	sample_conditions_1
3D 15N-separated NOESY	sample_1	isotropic	sample_conditions_1

Software:

NMRPipe v11.5 - processing

Poky - chemical shift assignment

NMR spectrometers:

Bruker AVANCE III 600 MHz
Bruker AVANCE III 800 MHz
Bruker AVANCE III 850 MHz

BMRB Entry 52000