BMRB Entry 18015
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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/BMR18015
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Title: Chemical shift assignments for the homeodomain of Pitx2 in complex with a TAATCC DNA binding site
Deposition date: 2011-10-21 Original release date: 2011-11-28
Authors: Baird-Titus, Jamie; Doerdelmann, Thomas; Chaney, Beth; Clark-Baldwin, Kimber; Dave, Vrushank; Ma, Jun
Citation: Chaney, Beth; Clark-Baldwin, Kimber; Dave, Vrushank; Ma, Jun; Rance, Mark. "Solution structure of the K50 class homeodomain PITX2 bound to DNA and implications for mutations that cause Rieger syndrome" Biochemistry 44, 7497-7511 (2005).
Assembly members:
PITX2, polymer, 68 residues, 8486.608 Da.
DNA_1, polymer, 11 residues, 3229.152 Da.
DNA_2, polymer, 11 residues, 3478.311 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):
PITX2: GSQRRQRTHFTSQQLQELEA
TFQRNRYPDMSTREEIAVWT
NLTEARVRVWFKNRRAKWRK
REEFIVTD
DNA_1: CTCTAATCCCC
DNA_2: GGGGATTAGAG
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 225 |
| 15N chemical shifts | 89 |
| 1H chemical shifts | 519 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | PITX2 | 1 |
| 2 | DNA_1 | 2 |
| 3 | DNA_2 | 3 |
Entities:
Entity 1, PITX2 68 residues - 8486.608 Da.
Residues 61-66 represent a non-native cloning artifact. Residues -2, -1 represent are non-native, cloning artifact.
| 1 | GLY | SER | GLN | ARG | ARG | GLN | ARG | THR | HIS | PHE | ||||
| 2 | THR | SER | GLN | GLN | LEU | GLN | GLU | LEU | GLU | ALA | ||||
| 3 | THR | PHE | GLN | ARG | ASN | ARG | TYR | PRO | ASP | MET | ||||
| 4 | SER | THR | ARG | GLU | GLU | ILE | ALA | VAL | TRP | THR | ||||
| 5 | ASN | LEU | THR | GLU | ALA | ARG | VAL | ARG | VAL | TRP | ||||
| 6 | PHE | LYS | ASN | ARG | ARG | ALA | LYS | TRP | ARG | LYS | ||||
| 7 | ARG | GLU | GLU | PHE | ILE | VAL | THR | ASP |
Entity 2, DNA_1 11 residues - 3229.152 Da.
| 1 | DC | DT | DC | DT | DA | DA | DT | DC | DC | DC | ||||
| 2 | DC |
Entity 3, DNA_2 11 residues - 3478.311 Da.
| 1 | DG | DG | DG | DG | DA | DT | DT | DA | DG | DA | ||||
| 2 | DG |
Samples:
sample_1: PITX2, [U-99% 13C; U-99% 15N], 1 mM; DNA_1 1 mM; DNA_2 1 mM; H2O, [U-99% 13C; U-99% 15N], 90%; D2O, [U-99% 13C; U-99% 15N], 10%
sample_2: PITX2, [U-99% 15N], 1 mM; DNA_1 1 mM; DNA_2 1 mM; H2O, [U-99% 13C; U-99% 15N], 90%; D2O, [U-99% 13C; U-99% 15N], 10%
sample_conditions_1: pH: 7.0; pressure: 1 atm; temperature: 295 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D C(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D H(CCO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | 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 HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
Software:
CYANA, Guntert, Mumenthaler and Wuthrich - structure solution
AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement
NMR spectrometers:
- Varian INOVA 800 MHz
- Varian INOVA 600 MHz
- Varian INOVA 500 MHz
Related Database Links:
| BMRB | 17145 17147 17452 |
| PDB | |
| DBJ | BAA75247 BAA75248 BAB69053 BAD12775 BAF84280 |
| EMBL | CAA06696 CAA06697 CAA09455 CAB52283 CAB52284 |
| GB | AAB38505 AAB38864 AAB87380 AAC16257 AAC24502 |
| REF | NP_000316 NP_001007500 NP_001017227 NP_001035436 NP_001035967 |
| SP | O35160 O75364 O93385 P81062 P97474 |
| TPG | DAA14908 DAA28868 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts