BMRB Entry 27366
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR27366
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Title: Backbone 1H, 15N chemical shift assignments of Kaiso E535Q zinc finger DNA binding domain in complex with its double CpG-methylated DNA consensus binding site (MeCG2) PubMed: 29546986
Deposition date: 2018-01-19 Original release date: 2018-03-22
Authors: Nikolova, Evgenia; Stanfield, Robyn; Dyson, H. Jane; Wright, Peter
Citation: Nikolova, Evgenia; Stanfield, Robyn; Dyson, H. Jane; Wright, Peter. "CH---O Hydrogen Bonds Mediate Highly Specific Recognition of Methylated CpG steps by the Zinc Finger Protein Kaiso" Biochemistry 57, 2109-2120 (2018).
Assembly members:
Kaiso_E535Q, polymer, 134 residues, Formula weight is not available
MeCG2_DNA, polymer, 18 residues, Formula weight is not available
entity_ZN, non-polymer, 65.409 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: pET21d
Entity Sequences (FASTA):
Kaiso_E535Q: MANKRMKVKHDDHYELIVDG
RVYYICIVCKRSYVCLTSLR
RHFNIHSWEKKYPCRYCEKV
FPLAQYRTKHEIHHTGERRY
QCLACGKSFINYQFMSSHIK
SVHSQDPSGDSKLYRLHPCR
SLQIRQYAYLSDRS
MeCG2_DNA: TGCTTCTXGXGAGAAGCA
- assigned_chemical_shifts
| Data type | Count |
| 15N chemical shifts | 111 |
| 1H chemical shifts | 111 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | Kaiso E535Q | 1 |
| 2 | DNA strand 1 | 2 |
| 3 | DNA strand 2 | 2 |
| 4 | Zinc ion 1 | 3 |
| 5 | Zinc ion 2 | 3 |
| 6 | Zinc ion 3 | 3 |
Entities:
Entity 1, Kaiso E535Q 134 residues - Formula weight is not available
| 1 | MET | ALA | ASN | LYS | ARG | MET | LYS | VAL | LYS | HIS | ||||
| 2 | ASP | ASP | HIS | TYR | GLU | LEU | ILE | VAL | ASP | GLY | ||||
| 3 | ARG | VAL | TYR | TYR | ILE | CYS | ILE | VAL | CYS | LYS | ||||
| 4 | ARG | SER | TYR | VAL | CYS | LEU | THR | SER | LEU | ARG | ||||
| 5 | ARG | HIS | PHE | ASN | ILE | HIS | SER | TRP | GLU | LYS | ||||
| 6 | LYS | TYR | PRO | CYS | ARG | TYR | CYS | GLU | LYS | VAL | ||||
| 7 | PHE | PRO | LEU | ALA | GLN | TYR | ARG | THR | LYS | HIS | ||||
| 8 | GLU | ILE | HIS | HIS | THR | GLY | GLU | ARG | ARG | TYR | ||||
| 9 | GLN | CYS | LEU | ALA | CYS | GLY | LYS | SER | PHE | ILE | ||||
| 10 | ASN | TYR | GLN | PHE | MET | SER | SER | HIS | ILE | LYS | ||||
| 11 | SER | VAL | HIS | SER | GLN | ASP | PRO | SER | GLY | ASP | ||||
| 12 | SER | LYS | LEU | TYR | ARG | LEU | HIS | PRO | CYS | ARG | ||||
| 13 | SER | LEU | GLN | ILE | ARG | GLN | TYR | ALA | TYR | LEU | ||||
| 14 | SER | ASP | ARG | SER |
Entity 2, DNA strand 1 18 residues - Formula weight is not available
| 1 | DT | DG | DC | DT | DT | DC | DT | 5CM | DG | 5CM | ||||
| 2 | DG | DA | DG | DA | DA | DG | DC | DA |
Entity 3, Zinc ion 1 - Zn - 65.409 Da.
| 1 | ZN |
Samples:
sample_1: Kaiso E535Q, [U-99% 15N], 0.2 mM; MeCG2 DNA 0.2 mM; TRIS 10 mM; TCEP 1 mM; H2O 95%; D2O 5%
sample_conditions_1: pH: 7.0; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
Software:
xwinnmr, Bruker Biospin - collection
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
SPARKY, Goddard - chemical shift assignment, data analysis
NMR spectrometers:
- Bruker DMX 800 MHz
Download HSQC peak lists in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts