BMRB Entry 16441
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR16441
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Title: Solution structure of the nucleotide binding domain of the human Menkes protein in the ATP-bound form PubMed: 19917612
Deposition date: 2009-08-05 Original release date: 2009-11-19
Authors: Banci, Lucia; Bertini, Ivano; Cantini, Francesca; Inagaki, Sayaka; Migliardi, Manuele; Rosato, Antonio
Citation: Banci, Lucia; Bertini, Ivano; Cantini, Francesca; Inagaki, Sayaka; Migliardi, Manuele; Rosato, Antonio. "The Binding Mode of ATP Revealed by the Solution Structure of the N-domain of Human ATP7A." J. Biol. Chem. 285, 2537-2544 (2010).
Assembly members:
N-MNK, polymer, 185 residues, 19803.387 Da.
ATP, non-polymer, 507.181 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):
N-MNK: SFTMHGTPVVNQVKVLTESN
RISHHKILAIVGTAESNSEH
PLGTAITKYCKQELDTETLG
TCIDFQVVPGCGISCKVTNI
EGLLHKNNWNIEDNNIKNAS
LVQIDASNEQSSTSSSMIID
AQISNALNAQQYKVLIGNRE
WMIRNGLVINNDVNDFMTEH
ERKGRTAVLVAVDDELCGLI
AIADT
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 675 |
| 15N chemical shifts | 193 |
| 1H chemical shifts | 1186 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | N-MNK | 1 |
| 2 | ATP | 2 |
Entities:
Entity 1, N-MNK 185 residues - 19803.387 Da.
After cleavage of the tag, four amino acids (SFTM) from the restriction site are left at the N-terminus of the protein.
| 1 | SER | PHE | THR | MET | HIS | GLY | THR | PRO | VAL | VAL | ||||
| 2 | ASN | GLN | VAL | LYS | VAL | LEU | THR | GLU | SER | ASN | ||||
| 3 | ARG | ILE | SER | HIS | HIS | LYS | ILE | LEU | ALA | ILE | ||||
| 4 | VAL | GLY | THR | ALA | GLU | SER | ASN | SER | GLU | HIS | ||||
| 5 | PRO | LEU | GLY | THR | ALA | ILE | THR | LYS | TYR | CYS | ||||
| 6 | LYS | GLN | GLU | LEU | ASP | THR | GLU | THR | LEU | GLY | ||||
| 7 | THR | CYS | ILE | ASP | PHE | GLN | VAL | VAL | PRO | GLY | ||||
| 8 | CYS | GLY | ILE | SER | CYS | LYS | VAL | THR | ASN | ILE | ||||
| 9 | GLU | GLY | LEU | LEU | HIS | LYS | ASN | ASN | TRP | ASN | ||||
| 10 | ILE | GLU | ASP | ASN | ASN | ILE | LYS | ASN | ALA | SER | ||||
| 11 | LEU | VAL | GLN | ILE | ASP | ALA | SER | ASN | GLU | GLN | ||||
| 12 | SER | SER | THR | SER | SER | SER | MET | ILE | ILE | ASP | ||||
| 13 | ALA | GLN | ILE | SER | ASN | ALA | LEU | ASN | ALA | GLN | ||||
| 14 | GLN | TYR | LYS | VAL | LEU | ILE | GLY | ASN | ARG | GLU | ||||
| 15 | TRP | MET | ILE | ARG | ASN | GLY | LEU | VAL | ILE | ASN | ||||
| 16 | ASN | ASP | VAL | ASN | ASP | PHE | MET | THR | GLU | HIS | ||||
| 17 | GLU | ARG | LYS | GLY | ARG | THR | ALA | VAL | LEU | VAL | ||||
| 18 | ALA | VAL | ASP | ASP | GLU | LEU | CYS | GLY | LEU | ILE | ||||
| 19 | ALA | ILE | ALA | ASP | THR |
Entity 2, ATP - C10 H16 N5 O13 P3 - 507.181 Da.
| 1 | ATP |
Samples:
sample_1: N-MNK, [U-99% 15N], 1.2 – 1.5 mM; ATP1.2 – 1.5 mM; phosphate 50 mM; DTT 2 mM; D2O 10%; H2O 90%
sample_2: N-MNK, [U-95% 13C; U-95% 15N], 0.8 – 1.0 mM; ATP0.8 – 1.0 mM; phosphate 50 mM; DTT 2 mM; D2O 10%; H2O 90%
sample_conditions_1: ionic strength: 0.05 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_2 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_2 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_2 | isotropic | sample_conditions_1 |
Software:
TOPSPIN, Bruker Biospin - collection
CARA, Keller and Wuthrich - chemical shift assignment
XEASY, Bartels et al. - data analysis
CYANA, Guntert, Mumenthaler and Wuthrich - structure solution
AMBER v10, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement
PSVS, Bhattacharya and Montelione - data analysis
ProcheckNMR, Laskowski and MacArthur - data analysis
NMR spectrometers:
- Bruker Avance 500 MHz
- Bruker Avance 700 MHz
- Bruker Avance 900 MHz
Related Database Links:
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts