BMRB Entry 34654

Name: Pre-catalytic complex of 10-23 DNAzyme with RNA target
Published: 2021-12-10

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PDB ID: 7pdu
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34654
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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:

Pre-catalytic complex of 10-23 DNAzyme with RNA target

Deposition date:

2021-08-07

Original release date:

2021-12-10

Authors:

Etzkorn, M.; Borggrafe, J.; Viegas, A.

Citation:

Citation: Borggrafe, Jan; Victor, Julian; Rosenbach, Hannah; Viegas, Aldino; Gertzen, Christoph; Wuebben, Christine; Kovacs, Helena; Gopalswamy, Mohanraj; Riesner, Detlev; Steger, Gerhard; Schiemann, Olav; Gohlke, Holger; Span, Ingrid; Etzkorn, Manuel. "Time-resolved structural analysis of an RNA-cleaving DNA catalyst" Nature 601, 144-149 (2022).
PubMed: 34949858

Assembly members:

Assembly members:
entity_1, polymer, 33 residues, 10266.592 Da.
entity_2, polymer, 19 residues, 5980.640 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: synthetic construct

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: TTGGGGTAAGGCTCGCTACA ACGAGGTGCATGT
entity_2: ACAUGCACCGUUACCCCAA

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
13C chemical shifts	118
15N chemical shifts	6
1H chemical shifts	423

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	2

Entities:

Entity 1, unit_1 33 residues - 10266.592 Da.

1

DT

DG

DT

DA

DG

2

DG

DC

DT

DC

DG

DC

DT

DA

DC

DA

3

DA

DC

DG

DA

DG

DT

DG

DC

DA

4

DT

DG

DT

Entity 2, unit_2 19 residues - 5980.640 Da.

1

A

C

A

U

G

C

A

C

G

2

U

A

C

A

Samples:

sample_1: 110-23 DNAzyme (33-MER) 500 uM; RNA target (19-MER) 500 uM; Tris-d11 50 mM; NaCl 100 mM; MgCl2 1 mM

sample_2: 110-23 DNAzyme (33-MER) 750 uM; RNA target (19-MER) 750 uM; Tris-d11 50 mM; NaCl 100 mM; MgCl2 1 mM

sample_3: 110-23 DNAzyme (33-MER), [U-13C; U-15N], 500 uM; RNA target (19-MER) 500 uM; Tris-d11 50 mM; NaCl 100 mM; MgCl2 1 mM

sample_conditions_1: ionic strength: 133 mM; pH: 7.5; pressure: 1 atm; temperature: 310.12 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC-TOCSY	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_3	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	anisotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1

Software:

TopSpin v4.0.6, Bruker Biospin - collection

CARA v1.9.1.5, Keller and Wuthrich - chemical shift assignment, peak picking

Sparky v3.114, Goddard - peak picking

X-PLOR NIH v2.49, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

NMR spectrometers:

Bruker AVANCE III HD 900 MHz
Bruker AVANCE III HD 750 MHz
Bruker AVANCE III HD 600 MHz