BMRB Entry 19511
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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/BMR19511
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Title: NMR Structure of the homeodomain transcription factor Gbx1 from Homo sapiens solved in the presence of the DNA sequence CGACTAATTAGTCG PubMed: 27396829
Deposition date: 2013-09-20 Original release date: 2013-09-30
Authors: Proudfoot, Andrew; Serrano, Pedro; Geralt, Michael; Wuthrich, Kurt
Citation: Proudfoot, Andrew; Geralt, Michael; Elsliger, Marc-Andre; Wilson, Ian; Wuthrich, Kurt; Serrano, Pedro. "Dynamic Local Polymorphisms in the Gbx1 Homeodomain Induced by DNA Binding" Structure 24, 1372-1379 (2016).
Assembly members:
Gbx1, polymer, 71 residues, 8346.782 Da.
DNA_1, polymer, 14 residues, Formula weight is not available
DNA_2, polymer, 14 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: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
Gbx1: SAPGGKSRRRRTAFTSEQLL
ELEKEFHCKKYLSLTERSQI
AHALKLSEVQVKIWFQNRRA
KWKRIKAGNVS
DNA_1: CGACTAATTAGTCG
DNA_2: CGACTAATTAGTCG
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 248 |
| 15N chemical shifts | 75 |
| 1H chemical shifts | 493 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | homeodomain transcription factor Gbx1 | 1 |
| 2 | DNA_1 | 2 |
| 3 | DNA_2 | 3 |
Entities:
Entity 1, homeodomain transcription factor Gbx1 71 residues - 8346.782 Da.
| 1 | SER | ALA | PRO | GLY | GLY | LYS | SER | ARG | ARG | ARG | ||||
| 2 | ARG | THR | ALA | PHE | THR | SER | GLU | GLN | LEU | LEU | ||||
| 3 | GLU | LEU | GLU | LYS | GLU | PHE | HIS | CYS | LYS | LYS | ||||
| 4 | TYR | LEU | SER | LEU | THR | GLU | ARG | SER | GLN | ILE | ||||
| 5 | ALA | HIS | ALA | LEU | LYS | LEU | SER | GLU | VAL | GLN | ||||
| 6 | VAL | LYS | ILE | TRP | PHE | GLN | ASN | ARG | ARG | ALA | ||||
| 7 | LYS | TRP | LYS | ARG | ILE | LYS | ALA | GLY | ASN | VAL | ||||
| 8 | SER |
Entity 2, DNA_1 14 residues - Formula weight is not available
| 1 | DC | DG | DA | DC | DT | DA | DA | DT | DT | DA | ||||
| 2 | DG | DT | DC | DG |
Entity 3, DNA_2 14 residues - Formula weight is not available
| 1 | DC | DG | DA | DC | DT | DA | DA | DT | DT | DA | ||||
| 2 | DG | DT | DC | DG |
Samples:
sample_1: Gbx1, [U-98% 13C; U-98% 15N], 0.8 mM; sodium chloride 50 mM; sodium phosphate 20 mM; sodium azide 5 mM; DNA_1 0.8 mM; DNA_2 0.8 mM; H2O 95%; D2O 5%
sample_conditions_1: ionic strength: 0.220 M; pH: 6.5; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aromatic | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| APSY 4D-HACANH | sample_1 | isotropic | sample_conditions_1 |
| APSY 5D-CBCACONH | sample_1 | isotropic | sample_conditions_1 |
| APSY 5D-HACACONH | sample_1 | isotropic | sample_conditions_1 |
Software:
CYANA, G ntert P., Keller and Wuthrich - chemical shift assignment, refinement
Opalp, Luginbuhl, Guntert, Billeter and Wuthrich - refinement
UNIO, Herrmann and Wuthrich - chemical shift assignment, structure solution
TOPSPIN, Bruker Biospin - collection, processing
NMR spectrometers:
- Bruker Avance 600 MHz
- Bruker Avance 800 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts