BMRB Entry 17574

Click here to enlarge.

PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17574
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Title:
Structure of a yeast RNase III dsRBD complex with a non-canonical RNA substrate provides new insights into substrate recognition
Deposition date:
2011-04-06
Original release date:
2011-08-03
Authors:
Wang, Zhonghua; Hartman, Elon; Roy, Kevin; Chanfreau, Guillaume; Feigon, Juli
Citation:

Citation: Wang, Zhonghua; Hartman, Elon; Roy, Kevin; Chanfreau, Guillaume; Feigon, Juli. "Structure of a yeast RNase III dsRBD complex with a non-canonical RNA substrate provides new insights into substrate recognition"  .

Assembly members:

Assembly members:
yeast RNase III dsRBD, polymer, 90 residues, 9822.442 Da.
non-canonical RNA substrate, polymer, 32 residues, Formula weight is not available

Natural source:

Natural source:   Common Name: baker's yeast   Taxonomy ID: 4932   Superkingdom: Eukaryota   Kingdom: Fungi   Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: PGEX-2T

Entity Sequences (FASTA):

Entity Sequences (FASTA):
yeast RNase III dsRBD: GSLDMNAKRQLYSLIGYASL RLHYVTVKKPTAVDPNSIVE CRVGDGTVLGTGVGRNIKIA GIRAAENALRDKKMLDFYAK QRAAIPRSES
non-canonical RNA substrate: GGGAUACCAUGUUCAAGUGA ACGUGGUAUCUC

Data sets:
Data typeCount
13C chemical shifts326
15N chemical shifts87
1H chemical shifts547

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1yeast RNase III dsRBD1
2non-canonical RNA substrate2

Entities:

Entity 1, yeast RNase III dsRBD 90 residues - 9822.442 Da.

1   GLYSERLEUASPMETASNALALYSARGGLN
2   LEUTYRSERLEUILEGLYTYRALASERLEU
3   ARGLEUHISTYRVALTHRVALLYSLYSPRO
4   THRALAVALASPPROASNSERILEVALGLU
5   CYSARGVALGLYASPGLYTHRVALLEUGLY
6   THRGLYVALGLYARGASNILELYSILEALA
7   GLYILEARGALAALAGLUASNALALEUARG
8   ASPLYSLYSMETLEUASPPHETYRALALYS
9   GLNARGALAALAILEPROARGSERGLUSER

Entity 2, non-canonical RNA substrate 32 residues - Formula weight is not available

1   GGGAUACCAU
2   GUUCAAGUGA
3   ACGUGGUAUC
4   UC

Samples:

sample_1: entity_1, [U-100% 13C; U-100% 15N], 0.8 – 1 mM; entity_21 – 2 mM; NaCl 150 mM; phosphate buffer 20 mM

sample_2: entity_1, [U-100% 13C; U-100% 15N], 0.8 – 1 mM; entity_21 – 2 mM; NaCl 150 mM; phosphate buffer 20 mM

sample_3: entity_10.8 – 1 mM; entity_2, [U-100% 13C; U-100% 15N], 1 – 2 mM; NaCl 150 mM; phosphate buffer 20 mM

sample_4: entity_10.8 – 1 mM; entity_2, [U-100% 13C; U-100% 15N], 1 – 2 mM; NaCl 150 mM; phosphate buffer 20 mM

sample_conditions_1: ionic strength: 0.15 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_4isotropicsample_conditions_1
2D 1H-1H NOESYsample_3isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D HCCH-COSYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
2D 1H-1H COSYsample_4isotropicsample_conditions_1
2D FILTERED/EDITED NOESYsample_4isotropicsample_conditions_1
2D 1H-15N HSQC IPAPsample_1isotropicsample_conditions_1

Software:

X-PLOR NIH v2.24, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

NMRView v5.2.2, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking

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

TALOS, Cornilescu, Delaglio and Bax - data analysis

TOPSPIN v2.0, Bruker Biospin - collection

xwinnmr, Bruker Biospin - collection

ProcheckNMR, Laskowski and MacArthur - data analysis

NMR spectrometers:

  • Bruker DRX 600 MHz
  • Bruker DRX 500 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks