BMRB Entry 27372

Name: 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)
Published: 2018-03-22

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR27372

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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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)

Deposition date:

2018-01-19

Original release date:

2018-03-22

Authors:

Nikolova, Evgenia; Stanfield, Robyn; Dyson, H. Jane; Wright, Peter

Citation:

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).
PubMed: 29546986

Assembly members:

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:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET21d

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
15N chemical shifts	114
1H chemical shifts	114

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Kaiso	1
2	DNA strand 1	2
3	DNA strand 2	3
4	Zinc ion 1	4
5	Zinc ion 2	4
6	Zinc ion 3	4

Entities:

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

1

MET

ALA

ASN

LYS

ARG

MET

LYS

VAL

LYS

HIS

2

ASP

HIS

TYR

GLU

LEU

ILE

VAL

ASP

GLY

3

ARG

VAL

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

GLU

TYR

ARG

THR

LYS

HIS

8

GLU

ILE

HIS

THR

GLY

GLU

ARG

TYR

9

GLN

CYS

LEU

ALA

CYS

GLY

LYS

SER

PHE

ILE

10

ASN

TYR

GLN

PHE

MET

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

DC

5CM

DG

5CM

2

DG

DA

DT

DA

DC

DG

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

1

DC

DG

DT

DA

DT

DC

DG

DC

2

DG

DA

DG

DC

DA

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:

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

SP	Q86T24
AlphaFold	Q8N3P0