Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR52574

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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: D43m3 holo-form
Published: 2026-02-23

Title:

D43m3 holo-form

Deposition date:

2024-07-31

Original release date:

2026-02-23

Authors:

Lee, Yun-Tzai; Stagno, Jason

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_TAC, non-polymer, 444.435 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: enzymatic semisynthesis

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	58
1H chemical shifts	40

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	D43m3	1
2	TETRACYCLINE	2

Entities:

Entity 1, D43m3 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, TETRACYCLINE - C22 H24 N2 O8 - 444.435 Da.

1

TAC

Samples:

sample_1: D43m3, [U-99% 15N], 300 uM; TETRACYCLINE 300 uM

sample_conditions_1: ionic strength: 0.01 M; pH: 6.5; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N TROSY	sample_1	isotropic	sample_conditions_1

Software:

NMRPipe - processing

SPARKY - chemical shift assignment

NMR spectrometers:

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

BMRB Entry 52574