BMRB Entry 52009
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR52009
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Title: Full assignment of 13C,15N-labeled oncogenic mutant human KRas4B-G12C(1-169) bound to GDP and free of Mg2+ ion at physiological pH PubMed: 37569478
Deposition date: 2023-06-28 Original release date: 2023-07-02
Authors: Gadanecz, Marton; Palfy, Gyula; Perczel, Andras
Citation: Gadanecz, Marton; Fazekas, Zsolt; Palfy, Gyula; Menyhard, Dora; Perczel, Andras. "NMR-Chemical-Shift-Driven Protocol Reveals the Cofactor-Bound, Complete Structure of Dynamic Intermediates of the Catalytic Cycle of Oncogenic KRAS G12C Protein and the Significance of the Mg2+ Ion" Int. J. Mol. Sci. 24, 12101-12101 (2023).
Assembly members:
entity_1, polymer, 169 residues, Formula weight is not available
entity_GDP, non-polymer, 443.201 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 Vector: pET-15b
Entity Sequences (FASTA):
entity_1: MTEYKLVVVGACGVGKSALT
IQLIQNHFVDEYDPTIEDSY
RKQVVIDGETCLLDILDTAG
QEEYSAMRDQYMRTGEGFLC
VFAINNTKSFEDIHHYREQI
KRVKDSEDVPMVLVGNKCDL
PSRTVDTKQAQDLARSYGIP
FIETSAKTRQGVDDAFYTLV
REIRKHKEK
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 463 |
| 15N chemical shifts | 158 |
| 1H chemical shifts | 906 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | KRAS-G12C | 1 |
| 2 | GDP | 2 |
Entities:
Entity 1, KRAS-G12C 169 residues - Formula weight is not available
| 1 | MET | THR | GLU | TYR | LYS | LEU | VAL | VAL | VAL | GLY | ||||
| 2 | ALA | CYS | GLY | VAL | GLY | LYS | SER | ALA | LEU | THR | ||||
| 3 | ILE | GLN | LEU | ILE | GLN | ASN | HIS | PHE | VAL | ASP | ||||
| 4 | GLU | TYR | ASP | PRO | THR | ILE | GLU | ASP | SER | TYR | ||||
| 5 | ARG | LYS | GLN | VAL | VAL | ILE | ASP | GLY | GLU | THR | ||||
| 6 | CYS | LEU | LEU | ASP | ILE | LEU | ASP | THR | ALA | GLY | ||||
| 7 | GLN | GLU | GLU | TYR | SER | ALA | MET | ARG | ASP | GLN | ||||
| 8 | TYR | MET | ARG | THR | GLY | GLU | GLY | PHE | LEU | CYS | ||||
| 9 | VAL | PHE | ALA | ILE | ASN | ASN | THR | LYS | SER | PHE | ||||
| 10 | GLU | ASP | ILE | HIS | HIS | TYR | ARG | GLU | GLN | ILE | ||||
| 11 | LYS | ARG | VAL | LYS | ASP | SER | GLU | ASP | VAL | PRO | ||||
| 12 | MET | VAL | LEU | VAL | GLY | ASN | LYS | CYS | ASP | LEU | ||||
| 13 | PRO | SER | ARG | THR | VAL | ASP | THR | LYS | GLN | ALA | ||||
| 14 | GLN | ASP | LEU | ALA | ARG | SER | TYR | GLY | ILE | PRO | ||||
| 15 | PHE | ILE | GLU | THR | SER | ALA | LYS | THR | ARG | GLN | ||||
| 16 | GLY | VAL | ASP | ASP | ALA | PHE | TYR | THR | LEU | VAL | ||||
| 17 | ARG | GLU | ILE | ARG | LYS | HIS | LYS | GLU | LYS |
Entity 2, GDP - C10 H15 N5 O11 P2 - 443.201 Da.
| 1 | GDP |
Samples:
sample_1: KRas4b G12C(1-169), [U-99% 13C; U-99% 15N], 0.85 mM; D2O, [U-100% 15N], 7%; DSS 1%; EDTA 10 mM; sodium chloride 140 mM; potassium chloride 2.7 mM; Na2HPO4 10 mM; KH2PO4 1.8 mM
sample_conditions_1: ionic strength: 0.15 M; pH: 7.4; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 4D HC(CC-TOCSY(CO))NH | sample_1 | isotropic | sample_conditions_1 |
| 4D 13C, 15N-edited SOFAST-HMQC-NOESY-SOFAST-HMQC (HCNH) | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_1 | isotropic | sample_conditions_1 |
Software:
TOPSPIN - collection, peak picking, processing
4D-CHAINS - chemical shift assignment
SPARKY - chemical shift assignment
CS-Rosetta - structure solution
GROMACS v2022.2 - refinement
NMR spectrometers:
- Bruker Avance 700 MHz
- Bruker Avance 700 MHz
- Bruker AVANCE NEO 900 MHz
Download HSQC peak lists in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts