BMRB Entry 18393
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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
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Title: The second dsRBD domain from A. thaliana DICER-LIKE 1 PubMed: 23194006
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: 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).
Assembly members:
dsRBD, polymer, 71 residues, 7961.290 Da.
Natural source: Common Name: Thale cress Taxonomy ID: 3702 Superkingdom: Eukaryota Kingdom: Viridiplantae Genus/species: Arabidopsis thaliana
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
dsRBD: NDICLRKNWPMPSYRCVKEG
GPAHAKRFTFGVRVNTSDRG
WTDECIGEPMPSVKKAKDSA
AVLLLELLNKT
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 309 |
| 15N chemical shifts | 67 |
| 1H chemical shifts | 475 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | dsRBD | 1 |
Entities:
Entity 1, dsRBD 71 residues - 7961.290 Da.
| 1 | ASN | ASP | ILE | CYS | LEU | ARG | LYS | ASN | TRP | PRO | ||||
| 2 | MET | PRO | SER | TYR | ARG | CYS | VAL | LYS | GLU | GLY | ||||
| 3 | GLY | PRO | ALA | HIS | ALA | LYS | ARG | PHE | THR | PHE | ||||
| 4 | GLY | VAL | ARG | VAL | ASN | THR | SER | ASP | ARG | GLY | ||||
| 5 | TRP | THR | ASP | GLU | CYS | ILE | GLY | GLU | PRO | MET | ||||
| 6 | PRO | SER | VAL | LYS | LYS | ALA | LYS | ASP | SER | ALA | ||||
| 7 | ALA | VAL | LEU | LEU | LEU | GLU | LEU | LEU | ASN | LYS | ||||
| 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:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_4 | isotropic | sample_conditions_2and3 |
| 3D HNCA | sample_4 | isotropic | sample_conditions_2and3 |
| 3D HNCACB | sample_4 | isotropic | sample_conditions_2and3 |
| 3D HN(CO)CA | sample_4 | isotropic | sample_conditions_2and3 |
| 3D HN(CO)CACB | sample_4 | isotropic | sample_conditions_2and3 |
| 3D HN(CA)CO | sample_4 | isotropic | sample_conditions_2and3 |
| 3D HN(CA)HA | sample_4 | isotropic | sample_conditions_2and3 |
| 3D H(CCO)NH | sample_4 | isotropic | sample_conditions_2and3 |
| 3D HCCH-TOCSY | sample_4 | isotropic | sample_conditions_2and3 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_3 | isotropic | sample_conditions_2and3 |
| 2D 1H-1H TOCSY | sample_3 | isotropic | sample_conditions_2and3 |
| 2D 15N-IPAP-HSQC | sample_2 | anisotropic | sample_conditions_2and3 |
| 3D HNHA | sample_4 | isotropic | sample_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 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts