BMRB Entry 34654

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:
Data typeCount
13C chemical shifts118
15N chemical shifts6
1H chemical shifts423

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22

Entities:

Entity 1, unit_1 33 residues - 10266.592 Da.

1   DTDTDGDGDGDGDTDADADG
2   DGDCDTDCDGDCDTDADCDA
3   DADCDGDADGDGDTDGDCDA
4   DTDGDT

Entity 2, unit_2 19 residues - 5980.640 Da.

1   ACAUGCACCG
2   UUACCCCAA

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:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_3isotropicsample_conditions_1
2D 1H-13C HSQC-TOCSYsample_3isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_3isotropicsample_conditions_1
2D 1H-1H NOESYsample_2anisotropicsample_conditions_1
2D 1H-1H TOCSYsample_2isotropicsample_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