BMRB Entry 25831
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/BMR25831
MolProbity Validation Chart
NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
NMR-STAR v2.1 text file (deprecated)
XML gzip file.
RDF gzip file.
All files associated with the entry
Title: solution structure of the complex of microRNA 20b pre-element with Rbfox RRM PubMed: 27001519
Deposition date: 2015-09-30 Original release date: 2016-04-12
Authors: Yang, Fan; Chen, Yu; Varani, Gabriele
Citation: Chen, Yu; Zubovic, Lorena; Yang, Fan; Godin, Katherine; Pavelitz, Tom; Castellanos, Javier; Macchi, Paolo; Varani, Gabriele. "Rbfox proteins regulate microRNA biogenesis by sequence-specific binding to their precursors and target downstream Dicer" Nucleic Acids Res. 44, 4381-4395 (2016).
Assembly members:
miR-20b, polymer, 23 residues, 7318.388 Da.
Rbfox_RRM, polymer, 104 residues, Formula weight is not available
Natural source: Common Name: human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens
Experimental source: Production method: T7 in vitro transcription Host organism: NA
Entity Sequences (FASTA):
miR-20b: GGUAGUUUUGGCAUGACUCU
ACC
Rbfox_RRM: GSHMNTENKSQPKRLHVSNI
PFRFRDPDLRQMFGQFGKIL
DVEIIFNERGSKGFGFVTFE
NSADADRAREKLHGTVVEGR
KIEVNNATARVMTNKKTVNP
YTNG
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 566 |
| 15N chemical shifts | 115 |
| 1H chemical shifts | 838 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | miR-20b | 1 |
| 2 | Rbfox_RRM | 2 |
Entities:
Entity 1, miR-20b 23 residues - 7318.388 Da.
| 1 | G | G | U | A | G | U | U | U | U | G | ||||
| 2 | G | C | A | U | G | A | C | U | C | U | ||||
| 3 | A | C | C |
Entity 2, Rbfox_RRM 104 residues - Formula weight is not available
| 1 | GLY | SER | HIS | MET | ASN | THR | GLU | ASN | LYS | SER | ||||
| 2 | GLN | PRO | LYS | ARG | LEU | HIS | VAL | SER | ASN | ILE | ||||
| 3 | PRO | PHE | ARG | PHE | ARG | ASP | PRO | ASP | LEU | ARG | ||||
| 4 | GLN | MET | PHE | GLY | GLN | PHE | GLY | LYS | ILE | LEU | ||||
| 5 | ASP | VAL | GLU | ILE | ILE | PHE | ASN | GLU | ARG | GLY | ||||
| 6 | SER | LYS | GLY | PHE | GLY | PHE | VAL | THR | PHE | GLU | ||||
| 7 | ASN | SER | ALA | ASP | ALA | ASP | ARG | ALA | ARG | GLU | ||||
| 8 | LYS | LEU | HIS | GLY | THR | VAL | VAL | GLU | GLY | ARG | ||||
| 9 | LYS | ILE | GLU | VAL | ASN | ASN | ALA | THR | ALA | ARG | ||||
| 10 | VAL | MET | THR | ASN | LYS | LYS | THR | VAL | ASN | PRO | ||||
| 11 | TYR | THR | ASN | GLY |
Samples:
sample_1: miR-20b 1 mM; sodium phosphate 10 mM; sodium chloride 20 mM; Rbfox RRM, [U-99% 13C; U-99% 15N], 1 mM; H2O 90%; D2O 10%
sample_2: miR-20b 1 mM; sodium phosphate 10 mM; sodium chloride 20 mM; Rbfox RRM, [U-99% 13C; U-99% 15N], 1 mM; D2O 100%
sample_3: miR-20b, [U-99% 13C; U-99% 15N], 1 mM; sodium phosphate 10 mM; sodium chloride 20 mM; Rbfox RRM 1 mM; D2O 100%
sample_4: miR-20b, [U-99% 13C; U-99% 15N], 1 mM; sodium phosphate 10 mM; sodium chloride 20 mM; Rbfox RRM 1 mM; H2O 90%; D2O 10%
sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 279 K
sample_conditions_2: pH: 6.5; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D F1-, F2-filtered 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D F1-, F2-filtered 1H-1H NOESY | sample_2 | isotropic | sample_conditions_2 |
| 2D 1H-1H TOCSY | sample_2 | isotropic | sample_conditions_2 |
| 2D 1H-13C HSQC | sample_2 | isotropic | sample_conditions_2 |
| 3D 1H-13C NOESY | sample_2 | isotropic | sample_conditions_2 |
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_2 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_2 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_2 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_2 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_2 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_2 |
| 3D HCCH-TOCSY | sample_2 | isotropic | sample_conditions_2 |
| 3D CCH-TOCSY | sample_2 | isotropic | sample_conditions_2 |
| 2D 1H-13C HSQC | sample_3 | isotropic | sample_conditions_2 |
| 3D 1H-13C NOESY | sample_3 | isotropic | sample_conditions_2 |
| 2D 1H-15N HSQC | sample_4 | isotropic | sample_conditions_1 |
| 3D 13C F1-filtered, F3-edited NOESY-HSQC | sample_2 | isotropic | sample_conditions_2 |
Software:
TOPSPIN, Bruker Biospin - collection
CYANA, Guntert, Mumenthaler and Wuthrich - structure solution
CcpNMR, CCPN - chemical shift assignment, data analysis, peak picking
AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
TALOS, Cornilescu, Delaglio and Bax - geometry optimization
NMR spectrometers:
- Bruker Avance 600 MHz
- Bruker Avance 800 MHz