BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 27372

Title: Backbone 1H, 15N chemical shift assignments of Kaiso zinc finger DNA binding domain in complex with a hemi-CpG-methylated DNA resembling the specific Kaiso binding site (KBS)   PubMed: 29546986

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 ., .-. (2018).

Assembly members:
Kaiso, polymer, 134 residues, Formula weight is not available
MeKBS_DNA_strand_1, polymer, 18 residues, Formula weight is not available
MeKBS_DNA_strand_2, 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

Entity Sequences (FASTA):
Kaiso: MANKRMKVKHDDHYELIVDG RVYYICIVCKRSYVCLTSLR RHFNIHSWEKKYPCRYCEKV FPLAEYRTKHEIHHTGERRY QCLACGKSFINYQFMSSHIK SVHSQDPSGDSKLYRLHPCR SLQIRQYAYLSDRS
MeKBS_DNA_strand_1: TGCTTCCXGXGAATAACG
MeKBS_DNA_strand_2: CGTTATTCGCGGGAAGCA

Data sets:
Data typeCount
15N chemical shifts114
1H chemical shifts114

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1Kaiso1
2DNA strand 12
3DNA strand 23
4Zinc ion 14
5Zinc ion 24
6Zinc ion 34

Entities:

Entity 1, Kaiso 134 residues - Formula weight is not available

1   METALAASNLYSARGMETLYSVALLYSHIS
2   ASPASPHISTYRGLULEUILEVALASPGLY
3   ARGVALTYRTYRILECYSILEVALCYSLYS
4   ARGSERTYRVALCYSLEUTHRSERLEUARG
5   ARGHISPHEASNILEHISSERTRPGLULYS
6   LYSTYRPROCYSARGTYRCYSGLULYSVAL
7   PHEPROLEUALAGLUTYRARGTHRLYSHIS
8   GLUILEHISHISTHRGLYGLUARGARGTYR
9   GLNCYSLEUALACYSGLYLYSSERPHEILE
10   ASNTYRGLNPHEMETSERSERHISILELYS
11   SERVALHISSERGLNASPPROSERGLYASP
12   SERLYSLEUTYRARGLEUHISPROCYSARG
13   SERLEUGLNILEARGGLNTYRALATYRLEU
14   SERASPARGSER

Entity 2, DNA strand 1 18 residues - Formula weight is not available

1   DTDGDCDTDTDCDC5CMDG5CM
2   DGDADADTDADADCDG

Entity 3, DNA strand 2 18 residues - Formula weight is not available

1   DCDGDTDTDADTDTDCDGDC
2   DGDGDGDADADGDCDA

Entity 4, Zinc ion 1 - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: Kaiso, [U-99% 15N], 0.2 mM; MeKBS_DNA_1 0.2 mM; MeKBS_DNA_2 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:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_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

Related Database Links:

SP Q86T24