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 18462

Title: Solution NMR structure of Kaiso zinc finger DNA binding domain in complex with Kaiso binding site DNA   PubMed: 22949637

Authors: Buck-Koehntop, Bethany; Stanfield, Robyn; Ekiert, Damian; Martinez-Yamout, Maria; Dyson, H. Jane; Wilson, Ian; Wright, Peter

Citation: Buck-Koehntop, Bethany; Stanfield, Robyn; Ekiert, Damian; Martinez-Yamout, Maria; Dyson, H. Jane; Wilson, Ian; Wright, Peter. "Molecular basis for recognition of methylated and specific DNA sequences by the zinc finger protein Kaiso."  Proc. Natl. Acad. Sci. U.S.A. 109, 15229-15234 (2012).

Assembly members:
Kaiso, polymer, 133 residues, 16086.681 Da.
DNA_strand_1, polymer, 19 residues, 5780.795 Da.
DNA_strand_2, polymer, 19 residues, 5869.857 Da.
ZINC ION, non-polymer, 65.409 Da.

Natural source:   Common Name: Humans   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: ANKRMKVKHDDHYELIVDGR VYYICIVCKRSYVCLTSLRR HFNIHSWEKKYPCRYCEKVF PLAEYRTKHEIHHTGERRYQ CLACGKSFINYQFMSSHIKS VHSQDPSGDSKLYRLHPCRS LQIRQYAYLSDRS
DNA_strand_1: GTGCTTCCTGCCAATAACG
DNA_strand_2: CGTTATTGGCAGGAAGCAC

Data sets:
Data typeCount
13C chemical shifts609
15N chemical shifts164
1H chemical shifts1288

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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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 133 residues - 16086.681 Da.

1   ALAASNLYSARGMETLYSVALLYSHISASP
2   ASPHISTYRGLULEUILEVALASPGLYARG
3   VALTYRTYRILECYSILEVALCYSLYSARG
4   SERTYRVALCYSLEUTHRSERLEUARGARG
5   HISPHEASNILEHISSERTRPGLULYSLYS
6   TYRPROCYSARGTYRCYSGLULYSVALPHE
7   PROLEUALAGLUTYRARGTHRLYSHISGLU
8   ILEHISHISTHRGLYGLUARGARGTYRGLN
9   CYSLEUALACYSGLYLYSSERPHEILEASN
10   TYRGLNPHEMETSERSERHISILELYSSER
11   VALHISSERGLNASPPROSERGLYASPSER
12   LYSLEUTYRARGLEUHISPROCYSARGSER
13   LEUGLNILEARGGLNTYRALATYRLEUSER
14   ASPARGSER

Entity 2, DNA_strand_1 19 residues - 5780.795 Da.

1   DGDTDGDCDTDTDCDCDTDG
2   DCDCDADADTDADADCDG

Entity 3, DNA_strand_2 19 residues - 5869.857 Da.

1   DCDGDTDTDADTDTDGDGDC
2   DADGDGDADADGDCDADC

Entity 4, ZINC ION_1 - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: Kaiso, [U-13C; U-15N], 500 uM; Kaiso binding sequence (KBS) 500 uM; Tris 10 mM; TCEP 1 mM; H2O 95%; D2O 5%

sample_2: Kaiso, [U-100% 13C; U-100% 15N; U-80% 2H], 500 uM; Kaiso binding sequence (KBS) 500 uM; Tris 10 mM; TCEP 1 mM; H2O 95%; D2O 5%

sample_3: Kaiso, [U-13C; U-15N], 500 uM; Kaiso binding sequence (KBS) 500 uM; Tris 10 mM; TCEP 1 mM; D2O 100%

sample_conditions_1: pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D HN(CO)CAsample_2isotropicsample_conditions_1
3D HCCH-COSYsample_3isotropicsample_conditions_1
3D CBCGCDsample_3isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_3isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1

Software:

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

CYANA, Guntert, Mumenthaler and Wuthrich - peak picking, refinement

NMRView, Johnson, One Moon Scientific - data analysis

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

TALOS, Cornilescu, Delaglio and Bax - chemical shift calculation

NMR spectrometers:

  • Bruker DMX 500 MHz
  • Bruker DMX 600 MHz
  • Bruker DMX 800 MHz
  • Bruker DMX 900 MHz
  • Bruker DRX 750 MHz

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