BMRB Entry 17883
Click here to enlarge.
PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR17883
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: The solution structure of the Lin28-ZnF domains bound to AGGAGAU of pre-let-7 miRNA PubMed: 22157959
Deposition date: 2011-08-25 Original release date: 2011-12-08
Authors: Allain, F.; Loughlin, F.
Citation: Loughlin, Fionna; Gebert, Luca; Towbin, Harry; Brunschweiger, Andreas; Hall, Jonathan; Allain, Frederic H-T. "Structural basis of pre-let-7 miRNA recognition by the zinc knuckles of pluripotency factor Lin28." Nat. Struct. Mol. Biol. 19, 84-89 (2012).
Assembly members:
Lin28-ZnF, polymer, 74 residues, 8033.417 Da.
AGGAGAU, polymer, 7 residues, 2284.459 Da.
ZN, non-polymer, 65.409 Da.
Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
Lin28-ZnF: SSGLVPRGSHMPKGKSMQKR
RSKGDRCYNCGGLDHHAKEC
KLPPQPKKCHFCQSISHMVA
SCPLKAQQGPSAQG
AGGAGAU: AGGAGAU
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 191 |
| 15N chemical shifts | 64 |
| 1H chemical shifts | 450 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | Lin-28 homolog A | 1 |
| 2 | hsa-pre-let-7g miRNA | 2 |
| 3 | ZINC ION | 3 |
Entities:
Entity 1, Lin-28 homolog A 74 residues - 8033.417 Da.
Residues 1-11 a non native expression tag
| 1 | SER | SER | GLY | LEU | VAL | PRO | ARG | GLY | SER | HIS | ||||
| 2 | MET | PRO | LYS | GLY | LYS | SER | MET | GLN | LYS | ARG | ||||
| 3 | ARG | SER | LYS | GLY | ASP | ARG | CYS | TYR | ASN | CYS | ||||
| 4 | GLY | GLY | LEU | ASP | HIS | HIS | ALA | LYS | GLU | CYS | ||||
| 5 | LYS | LEU | PRO | PRO | GLN | PRO | LYS | LYS | CYS | HIS | ||||
| 6 | PHE | CYS | GLN | SER | ILE | SER | HIS | MET | VAL | ALA | ||||
| 7 | SER | CYS | PRO | LEU | LYS | ALA | GLN | GLN | GLY | PRO | ||||
| 8 | SER | ALA | GLN | GLY |
Entity 2, hsa-pre-let-7g miRNA 7 residues - 2284.459 Da.
| 1 | A | G | G | A | G | A | U |
Entity 3, ZINC ION - Zn - 65.409 Da.
| 1 | ZN |
Samples:
sample_1: sodium acetate, [U-99% 2H], 10 ± 1 mM; beta-mercaptoethanol 1.5 ± .2 mM; ZnCl2 1.6 ± 0.1 mM; Lin28-ZnF, [U-99% 13C; U-99% 15N], 0.8 ± 0.1 mM; AGGAGAU 0.8 ± 0.1 mM; H2O 90%; D2O 10%
sample_2: sodium acetate, [U-99% 2H], 10 ± 1 mM; beta-mercaptoethanol 1.5 ± .2 mM; ZnCl2 1.6 ± 0.1 mM; Lin28-ZnF, [U-99% 13C; U-99% 15N], 0.8 ± 0.1 mM; AGGAGAU 0.8 ± 0.1 mM; D2O 100%
Sample_3: sodium acetate, [U-99% 2H], 10 ± 1 mM; beta-mercaptoethanol 1.5 ± .2 mM; ZnCl2 1.6 ± 0.1 mM; Lin28-ZnF, [U-99% 15N], 0.8 ± 0.1 mM; AGGAGAU 0.8 ± 0.1 mM; H2O 90%; D2O 10%
Sample_4: sodium acetate, [U-99% 2H], 10 ± 1 mM; beta-mercaptoethanol 1.5 ± .2 mM; ZnCl2 1.6 ± 0.1 mM; Lin28-ZnF, [U-10% 13C; U-99% 15N], 0.8 ± 0.1 mM; AGGAGAU 0.8 ± 0.1 mM; D2O 100%
sample_conditions_1: ionic strength: 10 mM; pH: 5.6; pressure: 1 atm; temperature: 303 K
sample_conditions_2: ionic strength: 10 mM; pH: 5.6; pressure: 1 atm; temperature: 283 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 3D_15N-separated_NOESY 3D_13C-separated_NOESY | Sample_3 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic | sample_2 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D H(CCO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_2 | isotropic | sample_conditions_1 |
| 2D-F1f-F2f-NOESY | sample_2 | isotropic | sample_conditions_1 |
| 2D-F2f-NOESY | sample_2 | isotropic | sample_conditions_1 |
| 3D-F3f-NOESY | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-15N HMQC | Sample_3 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | Sample_3 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | Sample_3 | isotropic | sample_conditions_2 |
| 2D 1H-13C HSQC | Sample_4 | isotropic | sample_conditions_1 |
| 3D-F3fe-NOESY | sample_1 | isotropic | sample_conditions_2 |
| 3D 1H-15N NOESY | Sample_3 | isotropic | sample_conditions_2 |
Software:
SPARKY, Goddard - chemical shift assignment
TOPSPIN, Bruker Biospin - collection, processing
CYANA v3.0, Guntert, Mumenthaler and Wuthrich - structure solution
AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement
NMR spectrometers:
- Bruker AV-III 500 MHz
- Bruker AV-III 600 MHz
- Bruker AV-III 700 MHz
- Bruker Avance 900 MHz
Related Database Links:
| PDB | |
| DBJ | BAB14075 BAI46599 |
| GB | AAH28566 AAM77751 ABM84324 ABM87718 AIC52303 |
| REF | NP_001102739 NP_078950 XP_001114640 XP_002716148 XP_002720890 |
| SP | Q9H9Z2 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts