BMRB Entry 30305
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30305
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Title: Solution structure of C2 domain from protein kinase C alpha in ternary complex with calcium and V5-pHM peptide PubMed: 29642029
Deposition date: 2017-06-12 Original release date: 2018-04-20
Authors: Yang, Y.; Igumenova, T.
Citation: Yang, Yuan; Shu, Chang; Li, Pingwei; Igumenova, Tatyana. "Structural basis of protein kinase C alpha regulation by the C-terminal tail" Biophys. J. 114, 1590-1603 (2018).
Assembly members:
Protein kinase C alpha type, polymer, 139 residues, 16240.451 Da.
V5-pHM peptide, polymer, 12 residues, 1298.187 Da.
CALCIUM ION, non-polymer, 40.078 Da.
Natural source: Common Name: Rat Taxonomy ID: 10116 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Rattus norvegicus
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
Protein kinase C alpha type: HTEKRGRIYLKAEVTDEKLH
VTVRDAKNLIPMDPNGLSDP
YVKLKLIPDPKNESKQKTKT
IRSTLNPQWNESFTFKLKPS
DKDRRLSVEIWDWDRTTRND
FMGSLSFGVSELMKMPASGW
YKLLNQEEGEYYNVPIPEG
V5-pHM peptide: XDQSDFEGFXYX
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 59 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
| 2 | entity_2 | 2 |
| 3 | entity_3, 1 | 3 |
| 4 | entity_3, 2 | 3 |
Entities:
Entity 1, entity_1 139 residues - 16240.451 Da.
| 1 | HIS | THR | GLU | LYS | ARG | GLY | ARG | ILE | TYR | LEU | ||||
| 2 | LYS | ALA | GLU | VAL | THR | ASP | GLU | LYS | LEU | HIS | ||||
| 3 | VAL | THR | VAL | ARG | ASP | ALA | LYS | ASN | LEU | ILE | ||||
| 4 | PRO | MET | ASP | PRO | ASN | GLY | LEU | SER | ASP | PRO | ||||
| 5 | TYR | VAL | LYS | LEU | LYS | LEU | ILE | PRO | ASP | PRO | ||||
| 6 | LYS | ASN | GLU | SER | LYS | GLN | LYS | THR | LYS | THR | ||||
| 7 | ILE | ARG | SER | THR | LEU | ASN | PRO | GLN | TRP | ASN | ||||
| 8 | GLU | SER | PHE | THR | PHE | LYS | LEU | LYS | PRO | SER | ||||
| 9 | ASP | LYS | ASP | ARG | ARG | LEU | SER | VAL | GLU | ILE | ||||
| 10 | TRP | ASP | TRP | ASP | ARG | THR | THR | ARG | ASN | ASP | ||||
| 11 | PHE | MET | GLY | SER | LEU | SER | PHE | GLY | VAL | SER | ||||
| 12 | GLU | LEU | MET | LYS | MET | PRO | ALA | SER | GLY | TRP | ||||
| 13 | TYR | LYS | LEU | LEU | ASN | GLN | GLU | GLU | GLY | GLU | ||||
| 14 | TYR | TYR | ASN | VAL | PRO | ILE | PRO | GLU | GLY |
Entity 2, entity_2 12 residues - 1298.187 Da.
| 1 | ACE | ASP | GLN | SER | ASP | PHE | GLU | GLY | PHE | SEP | ||||
| 2 | TYR | NH2 |
Entity 3, entity_3, 1 - Ca - 40.078 Da.
| 1 | CA |
Samples:
sample_1: C2 domain of protein kinase C alpha, [U-13C; U-15N], 0.89 mM; CALCIUM ION 2.225 mM; MES 6.7 mM; V5-pHM peptide 2 mM; potassium chloride 67 mM; sodium azide 0.2 mg/mL
sample_2: C2 domain of protein kinase C alpha, [U-13C; U-15N], 1.47 mM; CALCIUM ION 3.75 mM; MES 6.7 mM; V5-pHM peptide 0.6 mM; potassium chloride 67 mM; sodium azide 0.2 mg/mL
sample_3: C2 domain of protein kinase C alpha, [U-13C; U-15N], 0.89 mM; CALCIUM ION 2.225 mM; MES 6.7 mM; V5-pHM peptide 2 mM; potassium chloride 67 mM; sodium azide 0.2 mg/mL
sample_conditions_1: ionic strength: 0.076 M; pH: 6.0; pressure: 1 atm; temperature: 296.15 K
sample_conditions_2: ionic strength: 0.077 M; pH: 6.0; pressure: 1 atm; temperature: 296.15 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_2 | isotropic | sample_conditions_2 |
| 2D 1H-13C HSQC aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_3 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic | sample_3 | isotropic | sample_conditions_1 |
| 3D HCCH-COSY | sample_3 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D H(CCO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D C(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D aromatic HCCH-TOCSY | sample_3 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_3 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D [F2-15N,13C filtered] NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D [F2-15N,13C filtered] NOESY | sample_3 | isotropic | sample_conditions_1 |
| 2D [F1,F2-15N,13C filtered] NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D [F1,F2-15N,13C filtered] NOESY | sample_2 | isotropic | sample_conditions_2 |
| 2D [F1,F2-15N,13C filtered] TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 2D [F1,F2-15N,13C filtered] TOCSY | sample_2 | isotropic | sample_conditions_2 |
| 3D [F1-15N,13C filtered] 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D [F1-15N,13C filtered] 1H-13C NOESY | sample_3 | isotropic | sample_conditions_1 |
Software:
ARIA, Linge, O'Donoghue and Nilges - structure calculation
CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement
HADDOCK, Bonvin - structure calculation
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
SPARKY, Goddard - chemical shift assignment
TOPSPIN, Bruker Biospin - collection
NMR spectrometers:
- Bruker AvanceIII 800 MHz
- Bruker AvanceIII 600 MHz
- Bruker AvanceIII 500 MHz