BMRB Entry 18393

Click here to enlarge.

PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18393
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:
The second dsRBD domain from A. thaliana DICER-LIKE 1
Deposition date:
2012-04-12
Original release date:
2013-01-22
Authors:
Burdisso, Paula; Suarez, Irina; Bersch, Beate; Bologna, Nicolas; Palatnik, Javier; Boisbouvier, Jerome; Rasia, Rodolfo
Citation:

Citation: Burdisso, Paula; Suarez, Irina; Bologna, Nicolas; Palatnik, Javier; Bersch, Beate; Rasia, Rodolfo. "Second double-stranded RNA binding domain of dicer-like ribonuclease 1: structural and biochemical characterization."  Biochemistry 51, 10159-10166 (2012).
PubMed: 23194006

Assembly members:

Assembly members:
dsRBD, polymer, 71 residues, 7961.290 Da.

Natural source:

Natural source:   Common Name: Thale cress   Taxonomy ID: 3702   Superkingdom: Eukaryota   Kingdom: Viridiplantae   Genus/species: Arabidopsis thaliana

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET-TEV

Entity Sequences (FASTA):

Entity Sequences (FASTA):
dsRBD: NDICLRKNWPMPSYRCVKEG GPAHAKRFTFGVRVNTSDRG WTDECIGEPMPSVKKAKDSA AVLLLELLNKT

Data sets:
Data typeCount
13C chemical shifts309
15N chemical shifts67
1H chemical shifts475

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1dsRBD1

Entities:

Entity 1, dsRBD 71 residues - 7961.290 Da.

1   ASNASPILECYSLEUARGLYSASNTRPPRO
2   METPROSERTYRARGCYSVALLYSGLUGLY
3   GLYPROALAHISALALYSARGPHETHRPHE
4   GLYVALARGVALASNTHRSERASPARGGLY
5   TRPTHRASPGLUCYSILEGLYGLUPROMET
6   PROSERVALLYSLYSALALYSASPSERALA
7   ALAVALLEULEULEUGLULEULEUASNLYS
8   THR

Samples:

sample_1: dsRBD, [U-100% 13C; U-100% 15N], 800 mM; HEPES 50 mM; sodium azide 0.05%; PMSF 1 mM; H2O 90%; D2O 10%

sample_2: dsRBD, [U-100% 13C; U-100% 15N], 600 uM; sodium phosphate 50 mM; C12/E5-Hexanol 5%; DTT 10 mM; PMSF 1 mM; sodium azide 0.05%; sodium chloride 50 mM; H2O 90%; D2O 10%

sample_3: dsRBD 800 mM; sodium phosphate 50 mM; sodium chloride 50 mM; sodium azide 0.05%; PMSF 1 mM; D2O 100%

sample_4: dsRBD, [U-100% 13C; U-100% 15N], 600 mM; sodium phosphate 100 mM; sodium chloride 50 mM; sodium azide 0.05%; PMSF 1 mM; DTT 10 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.05 M; pH: 7; pressure: 1 atm; temperature: 298 K

sample_conditions_2and3: ionic strength: 0.75 M; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_4isotropicsample_conditions_2and3
3D HNCAsample_4isotropicsample_conditions_2and3
3D HNCACBsample_4isotropicsample_conditions_2and3
3D HN(CO)CAsample_4isotropicsample_conditions_2and3
3D HN(CO)CACBsample_4isotropicsample_conditions_2and3
3D HN(CA)COsample_4isotropicsample_conditions_2and3
3D HN(CA)HAsample_4isotropicsample_conditions_2and3
3D H(CCO)NHsample_4isotropicsample_conditions_2and3
3D HCCH-TOCSYsample_4isotropicsample_conditions_2and3
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_3isotropicsample_conditions_2and3
2D 1H-1H TOCSYsample_3isotropicsample_conditions_2and3
2D 15N-IPAP-HSQCsample_2anisotropicsample_conditions_2and3
3D HNHAsample_4isotropicsample_conditions_2and3

Software:

CNS, CCPN - refinement, structure solution

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

NMRView, Johnson, One Moon Scientific - chemical shift assignment

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Varian VXRS 800 MHz

Related Database Links:

PDB
DBJ BAD94606
EMBL CDX90002 CDY15207
GB AAF03534 AAF26461 AAG38019 AAG38020 AEE27220
REF NP_001184881 NP_171612 XP_002892088 XP_006306578 XP_006418369
SP Q9SP32
AlphaFold Q9SP32

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